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Quite often these days a new genetic index comes along that has been produced for breeders to use in their breeding plan. This month, August 2016, the new index is one that the Council on Dairy Cattle Breeding (CDCB) is calling Cow Livability (C.LIV). For breeders wanting their cows to live for many lactations, this will be a trait of interest.

What is Cow Livability?

CDCB is defining Cow Livability (C.LIV) as a prediction of a cow’s transmitting ability (aka genetic index) to remain alive while in the milking herd.

Every extended day that a cow remains milking in the herd gives the opportunity for more herd profit from more milk revenue and lower replacement costs. Cows that can remain alive when exiting the herd generating breeding stock or beef revenue, instead of the cost associated with deadstock disposal.

Facts About the USA Dairy Herd

It is interesting to note that CDCB reports that USA cow mortality rate averages 7% each lactation and death claims 20% of the USA cows while in the milking herd. On an annual basis that death loss costs the U.S. dairy farms $800 million or approximately $90 per milking cow per year.

How is C.LIV Different than PL?

CDCB provides the following explanation. “In contrast (to C.LIV), PL predicts how long a cow is expected to remain in the milking herd before dying or being culled.”

Livability is one of the traits that make up Productive Life, and it is economically important that cows remain alive, productive and not requiring another cow to replace her.

For decades, cow termination codes have been captured from DHIA herds with 32 million cows in CDCB’s database. Based on that extensive amount of data, CDCB has calculated correlations between C.LIV and PL of 0.70. So they are, in fact, different traits and breeders can expect to see that some sires may be ranked differently for the two traits.

Other Useful Traits

Already available, for a considerable time now, for breeders to use in breeding long-lived trouble free cows have been traits like PL and SCS.  But they only partially cover the spectrum of what breeders want to know. For instance, SCS does report the expected SCC level, but it does not cover if in fact a cow is able to resist mastitis. Each mastitis flare up, even though not life threatening, costs $400 (lost revenue, treatment, added labor, lost future production, etc.)  To address that, CDN now produces a genetic index for Mastitis Resistance. It includes factors (Read more: MASTITIS RESISTANCE SELECTION: NOW A REALITY!) beyond SCC.  Furthermore, Zoetis has now developed a Dairy Wellness Profit Index (DWP$) that is a genetic estimate of a cow’s ability to avoid or resist health problems or disease. (Read More: THE COMPLETE GUIDE TO UNDERSTANDING ZOETIS’ NEW WELLNESS TRAITS – CLARIFIDE® PLUS)

CDN has recently reported a three-year release plan for health and fertility traits.  In December 2016 it will publish a metabolic disease (ketosis & displaced abomasum) resistance index, in 2017 an index for resistance to fertility disorders (metritis & retained placenta) and in 2018 a hoof health index.

Considerable research is currently under way, and it will be interesting to see if breeds and/or bloodlines within breeds have different genetic capabilities for these added indexes. Many breeders feel that they detect differences between cow families for these various auxiliary traits.

What Do the Numbers Show for C.LIV?

The following CDCB table shows the importance of having high genetic indexes for individual traits when it comes to a sire having a high NM$ index.  All traits are directly or indirectly included the NM$ except for C.LIV.  That makes the comparison of C.LIV to NM$ truly independent.

Table 1 Average Genetic Index for USA AI Bulls (born after 1999), Grouped by Percent Rank for NM$

&RK for NM$Avg NM$Milk-lbsFat - lbsProtein-lbsDPRPLC.LIV
80 to 99588104352381.35.62.1
60 to 7942394434300.93.81.4
40 to 5931061225220.42.60.9
20 to 39197432181601.40.2
0 to 19-53-164-2-2-0.8-0.8-1.1

Soures: CDCB Article ” Genetic Evaluation for Cow Livability”

It is estimated by D Norman, CDCD and J Wright and P VanRaden, AIPL-USDA that having cows at 2.1 C.LIV compared to -1.1 C.LIV would be worth an additional annual net income of $9,400 (or $38.50 per cow) in the average USA DHIA herd of 244 cows.

CDCB reports that at some time in the future that C.LIV will be included in the four NM$ indexes replacing some of the current emphasis on PL. When that change is made CDCB sees the possibility that the combination of PL (14%) and C.LIV (7%) will move from the current 19% emphasis on PL in NM$ to 21% for PL plus C.LIV

Will These Functionality Traits Be Used?

For breeders that follow the concept of breeding for type and feeding for production, these functional traits are often regarded as a ho-hum issue.

However, for breeders wanting herds of cows that cause few problems, have minimal added expenses, and that remain in the herd a lactation or two longer than cows have in the past, then these additional traits, including C.LIV, will be important, when selecting the sires to buy semen from.

It is highly unlikely that there will be even one sire that is a standout for all functional traits. In fact, that is impossible. However, knowing bull ratings for added functional traits will allow breeds to avoid using sires that are below average for the traits that breeders find relevant to their breeding plan.

 The Bullvine Bottom Line

C.LIV is the latest, but certainly not the last, genetic index that will be available for breeders to use to breed functional, commercially profitable cows. Time will tell if it is useful. But the fact remains breeders need to consider all traits for which there are genetic indexes and then make informed choices about which ones to include in their sire selection plan.




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Who needs another index?

Tuesday, May 31st, 2016

Have you asked yourself or a fellow breeder that question? Genetic or management indexes are created for at least one reason or purpose.  It seems like every AI unit has developed their own index for one purpose or another.  Here are some Bullvine thoughts on multi-trait genetic indexes that are designed to assist breeders in genetic improvement and marketing. These indexes are usually referred to as total merit indexes.

Others Use Indexes

Read any business article and you will not get far without reading about the Dow Jones or Consumer Price indexes. Both are designed for specific purposes. They are to reflect the price trends in a selected group of companies on the NY Stock Market, or prices consumers must pay for a selected basket of goods that they usually purchase. We regularly hear whether they are trending upwards in inflationary times or down when the economy is trending negative. However, indexes do not end with the economy. Think about it – personal health indexes, student performance indexes, and equipment performance indexes all part of what we have in our daily lexicon.

Why Total Merit Indexes?

In the 1980’s, dairy cattle marketers were claiming to have the #1 bull or #1 cow in their country or the world. #1 for type, #1 for milk, or #1 for fat % improvement. Even then total animal improvement focused breeders were asking which animals put the total package together. As opposed to being single trait wonders.

In response, breeds and genetic evaluation centres saw the need for indexes that combined, on an appropriately weighted basis, the traits in need of improvement. In the United States, combined indexes like TPI, NM$ and JPI were created, and they came into wide use by breeders in their selection and marketing. In Canada, the index, created by all organizations working together, was LPI. Other country total merit indexes included BW in New Zealand, RZG in Germany, ISU in France and NVI in the Netherlands.

The principle behind all these indexes is that dairy cows are not bred with only one or two traits in mind. Some breeders indicate that having breeding indexes makes breeding dairy cattle more complicated. However, from our exposure to breeders, The Bullvine hears that having total merit indexes assists breeders who want to breed for lifetime profit or to compare animals before buying semen or embryos.

Blindly following a total merit index is not a good practice. Breeders need to know the purpose for which a total merit index is designed. BW (New Zealand) is designed for year round grazing and low body mass. JPI (American Jersey) is designed with an emphasis on milk solids production.

Breeders need to have goals and a herd breeding plan to make maximum use of total merit indexes. Readers may wish to refer to previous Bullvine articles when establishing a herd breeding plan ( Read more: What’s the plan?, 4 Steps to Faster Genetic Improvement, 8 Steps to Choosing What Sires to Use).  Breeders need to look five years into the future to decide what will be the criteria they will judge their females by. It is entirely possible if a breeder plans to operate his dairy farm business differently in the future than they have in the past, it could be time to use a different total merit index than they have utilized in the past.

Have Genetic Indexes Been Useful?

Annually CDCB and CDN publish reports showing ever increasing rates of genetic advancement for NM$ and LPI, respectively. In fact, a recent CDN article states that half of the gain in Canada can be attributed to increased genetic merit.

In the barns around the world, individual breeders are seeing gains in their cows’ ability for production, type and now SCS. When a breeder makes extensive use of sexed semen, it can be expected that 80% of a herd’s improvement can be attributed to the sires that have been used. Definitely having total merit index rankings three times a year gives breeders the opportunity to find new top sires and to eliminate bulls that may be high for one or two individual traits but in total are not able to do a complete job. Since the introduction of TPI and LPI, one of the outcomes has been that high type sires, with inferior production ability, are used very infrequently on a population basis.

Current Reality in Genetic Indexes

With many total merit indexes and many many individual trait indexes routinely published, it can be both time consuming and confusing to keep up-to-date.

Yet the fact is that the number of indexes is increasing with every index run. For example, in the past year, there have been three new trait indexes for mastitis resistance, fertility and feed efficiency. In 2015 new added total merit indexes were Pro$ (CDN) and DWP$(TM) (Zoetis), the latter being an index produced by a private company (Read more: Can you breed a healthier cow?, The Complete Guide to Understanding Zoetis’ New Wellness Traits – CLARIFIDE® Plus, Will Genetic Evaluations Go Private?)

Tomorrow’s Indexes

Every year new indexes for important traits for varying herd management systems will continue to come into the world of dairy cattle breeding. The following questions may assist breeders in deciding upon which genetic indexes to consider:

  • Is the new index designed for the way you plan to practice dairy farming?
  • Why would you not take the opportunity to use new relevant information?
  • Who can give you the most objective view of new genetic indexes?

One size does not fit all.  Not every new genetic index, total merit or individual trait, will assist a breeder in breeding an ever more profitable herd.

The Bullvine Bottom Line

Are there too many indexes? Only if you don’t have a breeding plan, and you don’t make the right choice of a total merit index for your herd. It is not about the total number of genetic indexes. In the end, it’s about being selective and only using what’s best for you.



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In current genetic evaluations, we lump data together, nationally and internationally. It is combined into one data set where we carry out the various analyzes to arrive at genetic indexes for all animals. But is that combining correct? Are there, in fact, any genetics by environment interactions situations that need consideration when combining data?  Should genetic evaluations be run separately for grazing herds compared to barn fed and housed herds?

What Does Cow Sense Tell Us?

Cow people know that there are some sire daughter groups and some cow families that perform differently when placed in different environments.

How often have you heard knowledgeable cow persons say – “He sires good useful barn cows but not enough show ring worthy daughters to have a PTAT of 3.21.” Or. “That cow family is great provided you go to the effort of pampering them like babies.”

Some Examples Where Proofs Have Not Always Told the Story

I have seen situations where sires’ daughters do not uniformly perform according to their indexes across all environments.

Quality Ultimate sired strength and stature as well as average milk and good fat percent, but he got the knock for not being tie stall friendly and lacking in daughter mobility in Canada, where he was proven. Yet in Australia breeders have told me that his mobility was not a problem. Why? Well, in Canada in tie stall barns with little to no access to exercise for 60% of the year, Ultimate daughters did not get the exercise they needed and so his proof was accurate, he had a feet and legs limitation. But, in Australia where cattle are outside walking on the ground all year, his daughter’s feet and legs were not a problem. (Read more: Mobility – The Achilles Heel of Every Breeding Program)

Looking beyond Ultimate, each of us can think of other bulls that may not suit all breeders’ needs. I think of Roybrook Starlite whose daughters were high yielders, but they often needed some special care and close monitoring. That is not something most commercial milk producers were prepared to do. Starlite’s maternal line had been a line bred family from a herd that took superb care of their animals.

Love Them or Hate Them

Today breeders either love or hate show bull Goldwyn and the commercial breeder’s dream bull, Oman. (Read more: Why Braedale Goldwyn Wasn’t a Great Sire of Sons)

A bull’s proof is an estimate of his average daughter. In extreme situations or environments, a bull’s proof may not be an accurate prediction of his true worth. How can breeders know if a bull will work, as his proof predicts, on their farm? Very little gets a breeder more upset that having a bull not perform in accordance with his proof.

Goldwyn in large commercially run groups of cows and Oman in the show ring are not good fits for what their proofs said should have ben expected.

Cow Indexes Open To More Environmental Influence

Of course, when it comes to cow indexes there are numerous examples of cows and cow families where the indexes are not accurate in predicting how they will breed on. (Read more: Has Genomics Knocked Out Hot House Herds?)

Now with genomic information included in genetic evaluations, the accuracies of prediction for cow indexes have been doubled and, therefore, may not be quite as variable in accuracy as they were in the past. Discerning breeders know that some cow families work best in certain single environments.

Points To Ponder

When conducting genetic evaluations, assumptions are made. Most of these assumptions have been shown to enhance the resulting genetic indexes. However here are a few assumptions that may contribute to inaccuracies when the indexes are used across all dairy farming situations.

  • Including Only Partial Herd Data
    Not including all contemporaries in type classification or herd recording data, when conducting BLUP genetic evaluations, violates the BLUP assumption that all animals are handled in a similar manner within a herd. Applying the results from selected data can lead to breeders questioning the daughters they get from a sire or cow family based on their genetic indexes.
  • Combining International Data Sets
    Definition of traits, variances within the data and methods of farm operation are different country to country. Interbull includes data from many production environments from many countries when doing its index calculations. Breeders should carefully interpret the results of combined international indexes when applying them back to their own herd environment.
  • Multiple Breeding Programs Within A Herd
    BLUP genetic evaluations assumes that only one breed program, one feeding program, and one management system exists in a single herd. If that assumption is violated then genetic evaluation results, especially cow indexes, can be less accurate than reported.
  • Sires Proven on Early Release Semen
    Most breeding companies release their high genomic young sires to themselves or selected herds six to nine months before it is made available to all breeders. It is imperative that the genetic evaluation procedures used for evaluating early release sires accurately adjusts for the genetic merit of the sire’s mates and the herds where the daughters are found.
  • Cows and Technology
    With many new technologies coming to market, breeders can expect to see genetic indexes for how cows adapt or perform within a technology. One such area is how cows work in single robotic milking farms. For example, breeders need to understand what is included when a bull’s daughters are called robot ready. Is that simply rear teat placement or does it include other factors as well (i.e. udder depth, milk let down, milking temperament, etc.)?
  • Genomic Information Not Yet Universal
    Even though the global dairy cattle breeding industry is almost into the ninth year of using genomic information, the genomic information and method of including the genomic results in genetic evaluations are not universal country to country. Breeders using genomic indexes from other countries need to do their homework before buying semen or embryos from abroad.

Does This Topic Need Attention?

The short answer is YES. To constructively improve their dairy cattle, breeders need to trust the numbers they use when making breeding decisions. Differences, biases, and inaccuracies in the data must be accounted for when conducting genetic evaluations.  As milk products become more of the global diet and as dairy cow populations expand, especially into more tropical conditions, breeders will need to know which cow families and sire daughter groups will work best in which environments.

The Bullvine Bottom Line

The genetic evaluations of tomorrow need to make sure that biases and inaccuracies are not created but rather eliminated when data sets are combined. The saying “Horses For Courses” comes to mind when considering bloodlines that will work better in one environment than another.



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For the first time, dairy producers can genetically select heifers to build a healthier herd.  But with this new ability comes the challenge of understanding Zoetis’ New Wellness Traits marketed at CLARIFIDE® Plus (Read more:  ZOETIS LAUNCHES CLARIFIDE® PLUS and Can you breed a healthier cow?).  In order to help you understand the power of this new tool here are some useful resources to guide you in your understanding.

Key Points

  • CLARIFIDE® Plus represents the first commercially available dairy genetic evaluation specifically designed for wellness traits in U.S. dairy cattle.
  • CLARIFIDE Plus genomic predictions for wellness traits provide reliable assessments of genetic risk factors for economically relevant health challenges in Holstein cattle.
  • The use of Dairy Wellness Profit Index (DWP$) would be expected to offer very similar selection emphasis to that achieved by Net Merit (NM$), making it a practical consideration for producers that have historically used NM$, but would like to apply additional selection emphasis on wellness traits.
  • CLARIFIDE Plus provides an expanded suite of genetic selection tools that provide highly relevant information to dairy producers who seek to incrementally improve the health, productivity and profitability of the dairy cattle they care for.

Genetic evaluation and selection in dairy cattle has largely focused on production traits such as milk and protein production. Indirect predictors of health and fertility (e.g.,somatic cell score, productive life, daughter pregnancy rate) are available and there is evidence to support some genetic improvement for these traits. However, presumably as a result of genetic antagonisms between production and health traits as well as changes in management practices, data supports increased incidence of many common diseases in contemporary dairy production systems. Consequently, dairy cows are considered to be less ‘robust’ than previous generations, which has serious implications for the health and fertility of the modern day dairy cow.

Profitable dairy cows are fertile, productive and require minimal extraneous inputs to maintain their health through all phases of production. They generally require fewer veterinary treatments or interventions, without compromising the health, welfare or economic efficiency of the cow, and are less likely to be prematurely culled. Genetic improvement programs that incorporate knowledge regarding differences in risk of disease into selection and breeding strategies have the potential to improve profitability of dairy production through improved prevention and control of economically relevant diseases as well as enhanced animal productivity.

Improving health and fitness traits, commonly referred to as functional or wellness traits, through genetic selection presents a compelling opportunity for dairy producers to help manage disease incidence and improve profitability when coupled with sound management practices. To date, direct predictors for wellness traits related to common disease conditions in dairy production have not been readily available in the U.S. CLARIFIDE® Plus represents the first commercially available dairy genetic evaluation specifically designed for wellness traits in U.S. dairy cattle, providing predictions describing the risk for six common diseases. Routine dehorning of commercial dairy cattle is also of concern for the industry as it relates to animal well-being and costs associated with routine dehorning methods. The selection and breeding of polled stock has been proposed as a strategy for proactively managing these concerns, including use of direct tests for polledness in cattle as well as including the economic benefits within selection indexes. CLARIFIED Plus includes the Zoetis Polled genomic test prediction in the offering to accurately identify and differentiate homozygous vs. heterozygous polled Holstein animals.



  • Mastitis, lameness, metritis, retained placenta, ketosis, displaced abomasum and other health events referred to as wellness traits have a significant impact on herd health, saleable milk and overall herd profitability.
  • Profitability is enhanced when the dairy has the advantage of mature cows that are productive for multiple lactations. To reach this longevity, cows must stay healthy and be reproductively sound, in addition to producing milk. Until now, management practices were the primary way to help cows either avoid or survive these health events.
  • CLARIFIDE Plus represents the first commercially available dairy genetic evaluation specifically designed for wellness traits in U.S. dairy cattle. Dairy producers can now genomically select heifers for wellness traits at an early age to help build a healthier herd.
  • CLARIFIDE Plus is the only genomic test that allows producers to rank animals with the new Dairy Wellness Profit IndexTM (DWP$TM) based on traits that affect health, performance and profit.
  • The use of Dairy Wellness Profit Index (DWP$) would be expected to offer similar selection emphasis to that achieved by Net Merit (NM$), making it a practical consideration for producers that have historically used NM$, but would apply additional selection emphasis on wellness traits.
  • CLARIFIDE Plus derives accurate genetic predictions for six new wellness traits derived using cutting‐ edge genetic evaluation methodology applied to data collected from millions of health records within U.S. commercial herds. This results in an average Reliability of 50% for the six traits.
  • Higher values are more desirable for all traits, thus selecting for a high Standardized Transmitting Abilities (STA) will apply selection pressure for reduced risk of disease.
  • In addition to wellness traits, CLARIFIDE Plus includes genetic information for the Zoetis propriety Polled trait.
  • DWP$ includes production, fertility, type, longevity and the dairy wellness traits, including polled test results.
  • Wellness Trait IndexTM (WT$TM) focuses on the wellness traits (Mastitis, Lameness, Metritis, Retained Placenta, Displaced Abomasum and Ketosis) in addition to Polled and estimates difference in expected lifetime profit associated with risk of disease.
  • DWP$ differs from other economic indexes because it includes direct predictions for economically important diseases. By including more characteristics affecting profitability, DWP$ describes more variation in profitability than other indexes.
  • With the use of DWP$, producers can potentially make more than $55 more profit per selected female over 10 years using a 15% culling selection strategy, even when test cost is higher than a NM$‐based ranking.

Development of Dairy Wellness Predictions

Genomic predictions for wellness traits were developed by Zoetis based on an independent database of pedigrees, genotypes and production records assembled from commercial dairies and internal assets. Health events were assembled from on-farm dairy production records provided with consent by commercial dairy producers. Data editing procedures to reduce recorded disease incidence to a common format were developed based on review of event codes in on-farm software and consultation with dairy production and veterinary experts. Targeted phenotypes included:

  • Mastitis (MAST)
  • Lameness (LAME)
  • Metritis (METR)
  • Retained placenta (RP)
  • Displaced abomasum (DA)
  • Ketosis (KET)
 All diseases were defined as a Holstein female diagnosed with the respective disease one or more times in a given lactation on the basis of qualifying event codes in on-farm dairy software in the case of commercial data, or clinical research records in the case of internal research assets. As of August 2015, the database used to derive CLARIFIED Plus predictions incorporated, primarily large commercial U.S. dairy operations from across the nation and included more than 10 million lactation records; 4 million cases of mastitis; 3 million cases each of metritis, retained fetal membranes, displaced abomasum, and lameness; more than 1.9 million cases of ketosis; and more than 15 million pedigree records. Additional records are continuously added to this database on a monthly basis from producer-supplied farm records.

Genomic data was obtained from commercially tested animals with owner consent or available genotypes within Zoetis research databases. More than 100,000 genotypes were available for consideration as of August 2015. Additional commercial genotypes are added on a weekly basis. Genotypes included in the evaluation were derived from both low and medium density genotypes, all imputed to Illumina®  BovineSNP50v2 using an internal imputation reference set and FImpute.CLARIFIDE Plus predictions are derived from a weekly internal genetic evaluation that employs single-step statistical methods for estimating genomic breeding values. This method for genetic evaluation derives a joint relationship matrix based on pedigree and genomic relationships and provides a unified framework that eliminates several assumptions and parameters, thus enabling more accurate genomic evaluations. Table 1 shows the average reliability of genomic predictions for wellness traits in CLARIFIDE Plus. Among approximately 29,901 Holstein heifers less than 2 years of age within the reference dataset, the average reliability was greater than or equal to 49% for all traits. Notably, as direct predictions for individual wellness traits are not presently available, this represents a substantial increase in reliability from zero. Further, the average reliability of genomic predictions for wellness traits continues to increase as more records are added to the evaluation.

Table 1 - clarifiedplus

Reporting of Wellness Traits in CLARIFIDE® Plus

CLARIFIDE® Plus predictions for wellness traits are expressed as genomic standardized transmitting abilities (STA), similar to how type traits are expressed. Values are centered at 100 with a standard deviation of 5. The reference population included 76,840 animals that had wellness predictions and CLARIFIDE results (Table 2). For all wellness trait predictions, a value of 100 represents average expected disease risk and values of greater than 100 reflect animals with lower expected average disease risk relative to herdmates with lower STA values. Higher values are more desirable for all traits, thus selecting for a high STA will apply selection pressure for reduced risk of disease.

Table 2 - clarifiedplus

CLARIFIDE Plus predictions for the Polled test will be reported as:

  • Tested homozygous polled: The genotype demonstrates that the animal is homozygous polled and will always produce a polled animal regardless of the horned status of the other parent.(Coded PP)
  • Polled carrier: The genotype reveals a heterozygous polled animal capable of producing a horned progeny. (Coded PC)
  • Tested free of polled (i.e., horned): The genotype is consistent with an animal that is horned. (Coded TP)
  • Indeterminate: The polled status of the animal cannot be definitively determined. (Coded I)

Two New Dairy Wellness Indexes

In addition to reporting of individual wellness traits, CLARIFIDE Plus also reports two economic selection indexes to inform selection decisions. Selection indexes are a critical component of many selection strategies as they provide a path for dairy producers to select for comprehensive genetic improvement across many economically important traits. The use of economic selection indexes helps to ensure that the distribution of selection pressure applied to component traits is appropriately balanced relative to the economic impact of the individual traits on dairy profitability. To support selection for reduced risk of disease in dairy females, two economic indexes were developed.

  • Wellness Trait Index (WT$): This multi-trait selection index exclusively focuses solely on the wellness traits1 (Mastitis,Lameness, Metritis, Retained Placenta, Displaced Abomasum, Ketosis and Polled) and directly estimates potential profit contribution of the wellness trait for an individual animal that will be passed onto the next generation.
  • Dairy Wellness Profit Index (DWP$): This multi-trait selection index includes production, fertility, type, longevity, calving ability, milk quality and the wellness traits, including Polled test results. By combining the wellness traits with those found in the current Net Merit (NM$) index, DWP$ directly estimates the potential profit contribution an individual animal will pass along to the next generation.

Table 3 - clarifiedplus copyThe economic indexes in CLARIFIDE Plus were derived using standard selection index theory. Economic assumptions were derived from those used in NM$ for the case of core traits, and from a review of peer-reviewed literature for wellness traits. Economic values for health traits that are considered in the derivation of NM$ were removed to avoid double-counting of the contributions of disease to dairy profitability. Economic values were then adjusted within the range of reported values based on the covariance among traits to achieve the final index weights.
To assess the extent to which use of CLARIFIDE Plus wellness trait indexes would alter selection emphasis relative to use of NM$, the expected response to selection per standard deviation of genetic improvement in the index was estimated. In examining the response of selection between DWP$ and NM$, it is clear that use of DWP$ will result  in greater genetic improvement in wellness traits and largely the same selection response for the rest of the traits. There is some decrease in selectionemphasis and expected genetic progress for production traits associated with the use of DWP$ (Table 3), which is consistent with our understanding of the relationship between increased production and disease risk. However, selection using DWP$ will increase milk, fat and protein production, just at a slightly lower genetic rate than would be achieved with alternative indexes that do not consider direct selection for wellness traits. Importantly, the use of DWP$ would be expected to offer very similar selection emphasis to that achieved by NM$, making it a practical consideration for producers who have historically used NM$ but would like to apply additional selection emphasis on wellness traits to achieve healthier, more profitable cows.

Table 4 defines the relative values for component traits in each of the two  wellness indexes. All indexes are expressed in a dollar value with higher positive numbers indicating the animal has the genetic potential to generate and transmit more profit over her lifetime.

Table 4 - clarifiedplus

CLARIFIDE® Plus Educational Videos 

  •  Improving Dairy Health and Profitability With CLARIFIDE® Plus in Holsteins
    CLARIFIDE Plus represents the first commercially available dairy genetic evaluation specifically designed for wellness traits in U.S. dairy cattle. Dairy producers now can genomically select heifers for wellness traits at an early age to build a healthier herd. Cheryl Marti, associate director of genetics and reproduction with Zoetis, provides an overview of the technology and how it benefits Holstein dairy producers.
  • Creating Wellness Trait Genomic Predictions
    Dr. Sue DeNise, executive director of VMRD genetics with Zoetis, describes the process and research that went into product development for the wellness traits associated with CLARIFIDE Plus.
  • Understanding How CLARIFIDE Plus Wellness Traits Are Reported
    Dr. Dan Weigel, director of Outcomes Research at Zoetis, describes the wellness traits associated with CLARIFIDE Plus and how the genetic results for each wellness trait are reported.
  • Exploring CLARIFIDE Plus Wellness Traits: Mastitis
    Mastitis is one of the most costly diseases on U.S. dairy herds. Dr. Gary Neubauer, senior manager of Dairy Technical Services, and Dr. Dan Weigel, director of Outcomes Research, discuss the genetic components of mastitis and how the wellness trait is reflected within CLARIFIDE Plus.
  • Exploring CLARIFIDE Plus Wellness Traits: Lameness
    Lameness is a widespread disorder among the U.S. dairy cattle population and has a significant impact on health and productivity. Two Zoetis technical services personnel — Dr. Gary Neubauer, senior manager of Dairy Technical Services, and David Erf, a Dairy Technical Services geneticist — provide an overview of the genetic component of the lameness wellness trait.
  • Exploring CLARIFIDE Plus Wellness Traits: Metritis and Retained Placenta
    Metritis and retained placenta are two significant disorders that impact fresh cows. Two Zoetis technical service personnel — Dr. Michael Lormore, director of Cattle and Equine Technical Services – Dairy, and Dr. Anthony McNeel, senior scientist with Global Genetics Technical Services — discuss the genetic components of these traits and how they are reflected within CLARIFIDE Plus outcomes.
  • Exploring CLARIFIDE® Plus Wellness Traits: Ketosis and Displaced Abomasum
    Two Zoetis technical service personnel — Dr. Michael Lormore, director of Cattle and Equine Technical Services – Dairy, and David Erf, a Dairy Technical Services geneticist — explore two traits included within the CLARIFIDE Plus offering: ketosis and displaced abomasum. The presentation details the significance of the two disorders and the genetic components of each trait.
  • The CLARIFIDE Plus Wellness Trait Index™ (WT$™)
    Brenda Reiter, a Global Genetics Technical Services scientist with Zoetis, provides an overview of the Wellness Trait Index (WT$). The index is a multitrait selection index that focuses specifically on genomic predictions for common health disorders of dairy cattle.
  • The Power of the Dairy Wellness Profit Index™ (DWP$™)
    CLARIFIDE Plus is the only genomic test that allows producers to rank animals with the Dairy Wellness Profit Index (DWP$) based on important traits that affect health, performance and profit. Dr. Jason Osterstock, director of Global Genetics Strategic Marketing with Zoetis, describes how DWP$ was developed and how dairy producers can use DWP$ to make more informed heifer selection decisions.
  • Strategies for Using the Dairy Wellness Profit Index™ (DWP$™)
    David Erf, a Dairy Technical Services geneticist with Zoetis, provides an overview of how to use the Dairy Wellness Profit Index (DWP$). The presentation outlines strategies dairy producers can use to implement DWP$ data to sort, select and mate Holstein dairy heifers.
  • Achieving Faster Genetic Progress with DWP$
    In traditional breeding programs without genomics, it can be challenging to make significant progress within traits that have low heritability. Dr. Dan Weigel, director of Outcomes Research at Zoetis, describes how faster genetic progress can be made through genomic technology by using direct selection of the new wellness traits and using DWP$ within CLARIFIDE Plus.
  • Achieving Dairy Wellness Outcomes with CLARIFIDE Plus
    Cheryl Marti, associate director of genetics and reproduction with Zoetis, provides an overview of the Zoetis Dairy Wellness outcomes approach and how CLARIFIDE Plus supports this process for healthy animals and healthy dairies

Frequently Asked Questions

Q: What health events will be covered by wellness trait predictions?
A: Common diseases in dairy cattle including mastitis, lameness, metritis, retained placenta, displaced abomasum and ketosis will be part of the wellness trait offering.

Q: Why do I need DWP$?
A: There are several reasons to utilize DWP$ in an effective genetic management strategy:
* DWP$ provides comprehensive, accurate and specific information on wellness traits to provide clarity and opportunity to make more profitable animal rankings and decisions.
* By including more characteristics affecting profitability, DWP$ describes more variation in profitability than other indexes.
* The use of DWP$ would be expected to offer very similar selection emphasis for production, reproduction and type traits as NM$ but with additional selection emphasis on wellness traits.

Q: As a dairy producer, if I select cattle based on their wellness trait profile, does that mean that they won’t get mastitis, metritis, etc.?
A: Risk of disease is influenced by genetic and environmental factors. CLARIFIDE Plus describes differences in the genetic risk factors, but genetic selection will not compensate for suboptimal management practices that may cause animals with apparent lower risk of disease to get sick. Producers should continue to use best management practices to prevent disease and apply CLARIFIDE Plus as another tool to improve dairy wellness.

Q: How long before I see a benefit to using these wellness traits?
A: The rate of Genetic progress depends on 4 factors—selection intensity, genetic variation, heritability and generation interval. Herds can make faster genetic progress by using DWP$ through greater selection pressure and higher genetic variation compared to NM$.

Q: How can I justify the investment in CLARIFIDE Plus?
A: The combination of wellness trait information and economic implications delivered through DWP$ provide dairy producers with powerful information that can be used to help build a healthier, more productive herd. With DWP$, producers get a more comprehensive ranking because of the additional differences in profitability described by including direct predictions for economically important health events such as mastitis, lameness, metritis, etc. By including more characteristics affecting profitability, DWP$ (offered only in CLARIFIDE Plus) describes more genetic variation in profitability than other indexes.

Q: How can I order the wellness trait predictions or find additional information?
A: Currently, CLARIFIDE Plus is only available for use in Holstein cattle. Holstein producers can order the CLARIFIDE Plus test through the order form at or via Enlight® . For more information, contact Zoetis Customer Service at 877‐233‐3362 or your Zoetis representative.


Dairy producers have enjoyed the availability of a comprehensive list of economically relevant traits and a robust genetic evaluation system to fuel their genetic improvement strategies. To date, a gap has existed in the ability to improve dairy profitability and dairy cow well-being through direct genetic selection for susceptibility to common diseases. CLARIFIDE® Plus provides accurate genetic predictions for wellness traits derived using cutting-edge genetic evaluation methodology applied to data collected from commercial production settings. The result is an expanded suite of genetic selection tools that provides highly relevant information to dairy producers that seek to continue to improve the health, productivity and profitability of the dairy cattle they care for.

Want to learn more?  Check out our upcoming webinar  “New Innovation in Genomic Selection to Reduce Disease Risks” presented with Zoetis on March 16th  & March 23rd

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Will Genetic Evaluations Go Private?

Wednesday, February 24th, 2016

Dairy cattle breeders have come to rely on their genetic indexes being calculated on a national or international basis by governments or independent industry organizations. Here at The Bullvine, we often refer to CDCB, CDN, VIT, ADHIS, Breed Societies and Interbull without mentioning their credentials or neutrality because we have trust in the numbers they produce for breeders to use to genetically advance their cattle. CDCB (Council on Dairy Cattle Breeding) in the USA is the newest of these organizations, and it has grown out of the AIPL-USDA’s decision to discontinue the production trait genetic indexing service for the US dairy cattle industry.

However, on the horizon is a considerable amount of on-farm data that national evaluation centers are not using. As well there is the desire by (A.I.) breeding companies to have and use genetic indexes for traits for which there is data but which may be outside the data standards that the national centres require or for which the companies do not wish to pay the fees charged by national centers. Add to that, new national trait evaluations are very slow in their development and approval.

So The Bullvine asks “Will genetic evaluations go private?”.

Private Is Not New

Privately produced trait rating systems have been around since the early days of A.I.  Breeders wanted to know facts, so A.I. organizations produced ratings starting with sire semen fertility followed by numerous other characteristics of their bulls’ daughters. One difficulty with these organization based systems was that each had its unique method of expression. This meant that breeders had to understand and remember many rating systems. It did, however, allow A.I.’s to have something unique in their tool box.

Another alternative, though perhaps not entirely private, is the improvement industry in New Zealand where LIC captures the data, calculates the genetic indexes, samples the bulls and markets the bulls. Arms length decision making and lack of diversity in the breeding program are questioned by breeders who use NZ genetics.

Data Standards

To do national and international genetic evaluations, where large volumes of data are included, it is paramount that the data combined have commonalities in such things as number of days milked, milking frequency, lactation number and age at classification. With the requirement for standardization, it results in the process of developing new genetic indexes being a relatively long process. That does not work well in a time of rapidly changing breeder needs for additional traits or when breeding companies have unique marketing plans.

Standardization adds cost. It is only worth it if the benefits for the population exceed the costs.

What Data Is Not Standardized?

Today there is a rapidly growing volume of data uniquely collected by companies. In the past half decade, the increase in the number of automated data capture devices has been dramatic. Rumination rate, animal activity, milking frequency, milk per quarter, milk temperature, hormone levels…it is almost an endless list. (Read more: BETTER DECISION MAKING BY USING TECHNOLOGY) And the list only gets longer every month. An important note is that each company and device has its method of data capture and expressing the results.

Another factor that breeders find confusing is that, although similarly named, traits are different in the ways that they are calculated and reported. Some of these traits include feed efficiency, fertility, length of herd life, ability to transition from dry to milking and mobility. It all depends on the organization, national genetic evaluation centre, breed society, A.I. or service company, doing the evaluation.

What Additional Indexes Could There Be?

Here again, the list of genetic indexes that could be possible is endless. A few that the Bullvine has heard breeders considering or organizations planning to produce include:

  • Milk let down and minutes to milk
  • Ability of animals to adapt to equipment and systems
  • Cow rejection rate in single unit robotic systems or cow visitation rate
  • Animal fertility including ability to conceive, early embryonic death and abortion rate
  • Animal behavior and social interaction
  • Feed intake and feed conversion
  • Animal mobility
  • Calf growth, health, feed conversion, disease resistance, .., etc.
  • Embryo production during embryo transfer
  • Ability to produce show winning progeny

Yes, the genetically related list is long. And beyond genetic indexes breeders will want many management and business related details. I received a novel question a month ago when a breeder ask if it could be possible for him to separate A1A1 and A1A2 milk from A2A2 milk, at milking time, so he would be able to keep the A2A2 milk separate for sale at a higher price. That’s a business person thinking about opportunities.

What is Likely to Happen

It is very likely that private companies with on-farm data and breeding companies wanting to have additional or unique indexes will form alliances for the calculation of new genetic indexes. If they aren’t doing it already, it will happen soon. Definitely, breeding companies working with equipment and service providers would be able to use all the data from many countries.

In the absence of having industry approved indexes breeders will be faced with using various company indexes. Fully trained geneticists already work for all of the data capture, breeding, service, product and genomic evaluation companies. So it is not a matter of if, but when it will happen.

Time will tell if these new genetic indexes are accurate, useful and understood. One significant question is – “Once the move to private is started will it continue to also include the current national evaluations for production, type, health and fertility traits?”.

In short “the horse is out of the barn”, there will be widespread availability of privately calculated genetic indexes in the future.

The Bullvine Bottom Line

Dairy cattle breeders can expect to see, read or hear sales reps promoting their sires based on new indexes. Is that good? The Bullvine predicts the answer is YES. Well, yes, provided that the indexes will assist breeders to improve the genetic merit of their cattle for lifetime profit.



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Discovering Genetic Anomalies from Genotyping

Wednesday, August 5th, 2015

Genotyping a single animal has direct advantages in terms of providing a genomic evaluation for genetic selection and mating as well as confirming its parentage for herdbook integrity. Accumulating thousands of genotypes for a population of animals in a breed has become an excellent source for identifying various genetic anomalies, which are usually undesirable. Although the discovery of an undesirable gene in a breed is initially viewed negatively, the new knowledge provides an opportunity to monitor the frequency over time and eventually eradicate it from the active population, especially among A.I. sires.

Haplotypes Impacting Fertility

Due to the growth of genotyping in North America since it began in 2008, the Canadian Dairy Network (CDN) database now includes over 800,000 Holstein genotypes and more than a million across all dairy breeds. This extensive database of DNA profiles allows scientists to follow the transmission of short sections of DNA strands, called haplotypes, from parent to progeny across generations. To date, given the number of genotyped animals in each breed, various “Haplotypes Impacting Fertility” have been identified including five in Holsteins (HH1 to
HH5), two in each of Jersey (JH1 and JH2) and Brown Swiss (BH1 and BH2) and one in Ayrshires (AH1). The impact of these haplotypes in each breed, which generally cause early embryonic death, depends on the frequency of the associated gene in the population and especially the percentage of active A.I. sires that are carriers. Any negative impact of these genetic anomalies can be eliminated by avoiding the mating of carrier sires to carrier heifers and cows, which is best achieved using computerised mating programs offered by A.I.

New Holstein Haplotype Discovered

Very recently, a group of research scientists in Germany discovered a new haplotype in the Holstein breed. Unlike the previously found “Haplotypes Impacting Fertility”, this particular genetic anomaly was found to be associated with calf survival in the first months of life. For calves that inherited the undesirable gene from both parents, it was found that they had an increased incidence of chronic/prolonged diarrhea that was untreatable, as well as other illnesses. Examination of blood samples from affected calves showed a cholesterol deficiency that prevented the normal deposition of fat in body tissues. Over the course of months after birth, the affected calves lost all body reserves and it appears that all eventually died.

In an attempt to identify the specific gene responsible for this newly identified genetic anomaly, the German scientists were successful in showing the inheritance pattern and the gene location being on chromosome 11. While the specific gene has not yet been located, a short series of SNPs, referred to as a haplotype, has been identified that is consistently present in the genotypes of carrier animals. Pedigree analysis of carriers has shown they all trace back to Maughlin Storm, born in 1991, as the oldest common genotyped sire. The popularity of Storm, as well as several of his outstanding sons and grandsons that are carriers, eventually spread the associated gene to many Holstein populations globally, which explains this discovery in Germany. Since the negative impact of this genetic anomaly, namely early calf death, only happens for calves that inherit the gene from both parents (i.e.: two descendants of Storm mated together), it takes multiple generations of breeding to discover.

A Complicating Factor

Unfortunately, without having an exact gene test for this genetic anomaly, determining the carrier status can be complicated for some animals. The haplotype identified in Storm and his carrier descendants also exists in Willowholme Mark Anthony (born in 1975) but he does not carry the specific undesirable gene. The presence of the common haplotype stems from the fact that Mark Anthony’s sire, Fairlea Royal Mark, is also the great maternal grandsire of Storm. It appears that somewhere in the transmission of genes from Fairlea Royal Mark down through the three generations to Storm a form of mutation occurred that caused this genetic anomaly. Without knowing the exact gene, the only tool available for identifying carriers is by using the defined haplotype. This means, however, that animals with both Storm and Mark Anthony in their pedigree may have the defined haplotype but could be falsely identified as a carrier of the responsible gene. Table 1 provides a list of the A.I. sires that are known carriers of this undesirable gene and have more that 5,000 registered daughters born in Canada to date. An animal with any of these sires in its pedigree may also be a carrier and genotyping such animals will help to clarify the carrier status.

Table 1: HCD Carrier Sires with over 5,000 Registered Daughters Born in Canada

Relationship to Maughlin Storm (HOCANM5457798)



Great Grandsons
















* Dudoc Mr Burns carries the haplotype with the undesirable gene from Storm as well as the haplotype sourced through Mark Anthony. Therefore, genotyping his progeny will not lead to conclusive results about the carrier status of the undesirable gene.

Carrier Probability Values

Since the initial discovery of the first “Haplotypes Impacting Fertility” CDN has been calculating and publishing “Carrier Probability” values for every animal in the CDN database. Regardless of the breed, the haplotype Carrier Probability values are displayed on the “Pedigree” link from each animal’s “Genetic Evaluation Summary” page on the CDN web site ( A displayed probability of 99% identifies animals that are expected to be “Carrier” while a value of 1% indicates they have been identified as “Free” based on the haplotype analysis. Animals not genotyped receive an estimated Carrier Probability that can vary from 99% to 1% depending on the probability values for its parents and other relatives.

In North America, this newly discovered haplotype in Holsteins will be labelled as HCD, meaning “Haplotype associated with Cholesterol Deficiency”. CDN has developed methodology for assigning a Carrier Probability value for HCD based on existing genotypes as well as tracking the source of the undesirable haplotype through pedigree analysis. This strategy allows some genotyped animals that have both Storm and Mark Anthony in their pedigree to be properly identified as “Carrier” or “Free” but for other animals, where this distinction in not possible, a Carrier Probability between 99% and 1% will be published by CDN.


In addition to genomic evaluations and integrity of pedigrees, accumulating thousands of genotypes for a given breed results in the discovery of new genetic anomalies. Scientists in Germany recently discovered a new “Haplotype associated with Cholesterol Deficiency” (i.e.:HCD) in Holsteins, which traces back to Maughlin Storm as the oldest genotyped sire of origin. Without the presence of an exact gene test to identify carriers, the current haplotype analysis can result in some animals being falsely labelled as a carrier if they have both Storm and Willowholme Mark Anthony in their pedigree. The methodology used by CDN to calculate the HCD Carrier Probability values (varying from 99% for “Carrier” to 1% for “Free”), reduces this problem by combining the haplotype test with pedigree analysis. Now that this undesirable anomaly is known, an industry effort can easily be made to reduce the frequency that carrier animals are mated together, thereby lowering the frequency that homozygous calves are born and subsequently die within months. The discovery of this genetic condition also demonstrates the value and importance of producers reporting to DHI the date and reason for every animal leaving the herd, including young calves.

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Dairy cattle farming has many numbers for breeders to review and weight as they go about their daily roles as manager, health care provider, bookkeeper, personnel manager, feed harvester, reproduction sequencer, animal selection or removal supervisor, ….. yes, the daily duty list is long. But in all cases, it is best to use a number when making a decision.

For this article, The Bullvine wishes to focus on the fact that science-based numbers (aka genetic indexes) are the best method to use when selecting the animals to produce the next generation.

Breeding – Is it Art or Science?

Dairy cattle breeders argue both sides of the answer to this question. Some breeders swear by a single observation, their impression or their experience (aka art) while others totally depend on science-based numbers. Let’s dig deeper.

What’s in the Number?

Breeders can use the number they can actually see, like lactation milk yield, or a cow’s milk genetic index that considers factors like age, herd mates, progeny, pedigree and now DNA analysis. The same applies to using a cow’s PTAT rather than her own classification.  It is best to consider all factors.

Can the Number be trusted?

Accuracy is paramount to success or failure in dairy cattle breeding. Making a breeding decision based a single individual observation is 20 to 25 percent accurate in predicting a cow’s progeny’s performance. Using a cow’s genetic index that includes pedigree, DNA analysis and performance will be sixty-five to seventy percent accurate.

Does the Number Mean Anything for You?

Every breeder needs to have a breeding plan (Read more: What’s the plan?) for their entire herd or an individual mating. In the plan, there needs to be the importance of individual traits. Not every trait, for which an index is available, is essential for every herd or mating. Indexes like gTPI and NM$ should be included in every plan.

Breed for Desired Outcome.

Higher Milk Revenue – Do you breed for protein yield or protein percent? Very definitely it is protein yield. It is the volume of protein that breeders are paid for. Higher protein percent is associated with less milk production.

Improving Herd Longevity – Do you select a genomic sire for his PL (Productive Life index) or how long his dam produced milk? Very definitely for his PL.  His dam’s length of life has many non-genetic factors and will have a very low heritability.

Improving Fertility – When mating a heifer do you consider her FI (Fertility Index) or the frequency with which her dam calved? Very definitely her FI.  Her dam’s calving interval has an extremely low heritability, almost zero.

Developing a High Type Herd – Do you select a sire based on PTAT or the number of show winners he produces? Very definitely his PTAT. Show herds do not use a wide spectrum of sires and do not randomly use sires, this results in potentially biased genetic evaluations on the sires they use.  Since many of the sires they are used on are not used in chimerical herds, the evaluations on these sires are biased.  When a “type” sire does cross into wide stream usage you start to see evaluations like Goldwyn’s.  Goldwyn is often noted as a great sire of show winners yet his PTAT of +1.81 and his PL of -0.5 reflects that used across the entire population he does not stand out as a significant improver.

The Bullvine Bottom Line

Genetic improvement depends upon using science to improve accuracy and the completeness of decision making. The rate of genetic advancement has improved significantly over the past decade, and the pace will double again in the next decade. Breeding is about science.



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Butlerview, Butler Feller Sales, Jetstream Genetics, Accelerated Genetics and Holstein World combined to put on an outstanding seminar on the current state of dairy cattle breeding.  Titled “Genetics in the Age of Genomics” and held at the beautiful Kierland Weston in Scottsdale Arizona, the seminar consisted of many of the top minds from around the world.  There where speakers from Research, A.I., and producers who combined managed over 30,000 milking cows.

  1. IMG_1541Welcome – Jeff Butler -Butlerview

    Jeff Butler, of Butlerview and Butler Fellers sales welcomes everyone to the Genetics in the Age of Genomics Conference in Scottsdale Arizona. Jeff and his team have brought together some of the greatest minds from across North America to share there thoughts about where the state of the dairy cattle genetics marketplace. Jeff also shares that Ed Fellers a key member of the team is unable to attend.  It was Ed who first introduced Jeff to genomics, telling him that it is Genomics that was going to change the breed.  Then a few weeks later Ed called Jeff and said “You are not going to believe this, but I own part of this bull and he is going to be a great genomic bull”.  His name was Atwood.  Atwood had 5 brothers and he was the last one, everyone else had been in there and taken all the other ones.  But this thing called “genomics” said that Atwood was going to be the best one of them all. In fact Atwood was the first genomic sire the Butler used. And they had some of the first Atwood calves on the ground.  It just so happens that two of them are named Adrianna, and Abrianna.  So as a result of these two early success stories and how Atwood was doing, and how genomics impacted the decisions to use Atwood Jeff was convinced on genomics.  While the old way was working ok, this “new way” was doing away better.(Read more: BUTLERVIEW: The Goals are Simple. The Genetics are Exceptional. and Exciting Times for Butlerview)Listen to how Jeff explains how dairy cattle genetics will help the dairy industry feed the world.

  2. IMG_1551Joao Durr – CEO of the Council on Dairy Cattle Breeding – Update on U.S. Genetic Evaluations: What’s to come?

    Joao Durr shares with us how CDCB operates, some of the major initiatives that they have coming up and how the US genetic evaluation system works as far as an operational sense.  Joao Durr brings a truly international perspective to the world of genetic evaluations having a background that involves many of the top dairy breeding countries as well as working at INTERBUL.

  3. IMG_1592Brian Van Doormal – GM Canadian Dairy Network – Profitable Genetics in Canada: What are your priorities?

    Brian Van Doormal has been the GM of the Canadian Dairy Network since its inception 20 years ago.  Brian highlights how CDN and other industry partners work together to help accelerate the Canadian dairy genetics industry.  Brian also shares with us some of the great work they have been doing to more accurately evaluate profitability, as well as identifying herd and daughter bias in genetics evaluations. (Read more: CANADIAN BULL PROOFS – You’ve Got to Prove It to Use It!)

  4. IMG_1604Dr. Dan Weigel, Zoetis – Genomics and the Commercial Dairyman

    Dr Weigel shares just how genomic testing has changed, but then also how much genomic testing can help all type of dairy operations.  Dr Weigel is able to bring an interesting perspective to the science of genomic testing, but also is a breeder of dairy cattle and able to put the science in a language that all dairy breeders can understand.  One of the key areas the Dr Wiegel shares is just how much performance difference producers can expect, especially based on how well managed their herds are.  During his presentation also makes it interactive for those in attendance, polling the audience about many of the key questions. (Read more: Herd Health, Management, Genetics and Pilot Projects: A Closer Look at ZOETIS)

  5. Breeder Panel Discussion – Our Options for the Future

    The panel consists of: John Andersen, Double A Dairy (JOHN ANDERSEN – COMMERCIAL and PEDIGREE – Building a Field of Dreams); Greg Andersen, Seagull Bay Dairy (“Breeding for Efficient Production and a Healthy Herd” with Greg Andersen from Seagull Bay – 2014 Holstein USA Distinguished Young Holstein Breeder); Greg Coyne, Coyne Farms; Don Bennink, North Florida Holsteins (NORTH FLORIDA HOLSTEINS. Aggressive, Progressive and Profitable!!). These 4 breeders represent over 30,000 milking cows, and all are invested in genetics and genomics.  This panel that is not afraid to share their thoughts about inbreeding, classification and the type of animals that commercial breeders are actually looking for.

  6. IMG_1629Dr George Wiggans – Research Leader, AIPL/ARS/USDA – Genomics and Where it Can Take Us

    Dr Wigeons shares with everyone the latest stats around inbreeding and genetic advancement. Dr George Wiggans from USDA shared with the group at the Genetics in Age of Genomics Conference that if you look at the top 100 bulls from 2012 (Dec 2012 NM$ compared to Dec 2014 NM$) the results are 94% accurate.

  7. AI Panel Discussion – Where Will the Bulls Come From?

    A great cross section of sire analysts from many of the top companies, including: Brian Carscadden – Semex Alliance; Paul Trapp – ABS Global; Lloyd Simon – Industry consultant; Ryan Weigal – Accelerated Genetics; Dan Bauer – Genex CRI & Jon Schefers – Alta Genetics. These gentlemen discuss inbreeding, polled, their selection process as well as where the industry is headed.

  8. The International Perspective Panel Discussion

    IMG_1702IMG_1704 IMG_1703
    To bring some international prospective to the discussion there is Jan DeVries – AI Total; Declan Patten – Australia; Paul Hunt – Alta Genetics.  These gentlemen represent not only many different countries but also many different roles in the industry.  From the COO of one of the largest AI companies, to a very successful entrepreneur to global dairy marketing expert.

  9. Dr. Tom Lawlor – Executive Director of Research & Development Holstein Association USA

    Dr Lawler shares with everyone some of the latest developments at HUSA, as well as an in-depth look into the state of inbreeding, herd profitability, and GTPI’s ability to predict actual profitability.



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It has been six years since genomic, genetic evaluations were introduced in North America.  Since that time, every part of the dairy improvement industry has changed. The business of artificial insemination has changed from selling predominantly proven sires and having to reward breeders for using young sires to young sire semen which now costs more than proven sire semen and accounts for more than half the semen sales.  On the one hand, there’s a growing misconception that genomics will replace traditional data recording systems, such as those offered by DHI and breed associations.  However, the reality is that, with genomics, accurate and complete performance data is required, in order to maintain the accuracy of genetic evaluations and allow a wider list of traits to be evaluated.

The question becomes where will that genetic information come from, if everyone stops classifying, registering and milk recording?

Accuracy comes from validating data with proven sires

Current genomic evaluations are more accurate than previous traditional evaluations primarily as a result of the large reference population of genotyped progeny proven sires. Without such a significant reference population, genomic evaluations would only offer small gains in accuracy compared to the significant move from 33% to 66% accuracy that a 50K genomic tested young sire currently receives.

The collection of performance data leads to a steady supply of new progeny proven bulls. Without these bulls continually expanding  the reference population, young bulls selected for A.I. would get further away  (and therefore less genetically related) from the proven sires in the reference population. Over time, this would negatively affect the accuracy of genomic evaluations, and we would actually start to see reliability figures decline.

Genomics have allowed us to make even faster genetic progress, however we still need field data for production, health, and conformation, in order to keep and even increase the reliability of the current genetic evaluation system.

Without genomics, test day records or a classification, a cow would maintain her Parent Average (PA) for all production and type traits for her entire life. She would thereby miss out on the opportunity to further enhance the accuracy of her genetic evaluations. Milk recording and classification data are added to the cow’s contribution from PA to produce an Estimated Breeding Value (EBV) that is more accurate than without it. For example, consider a first lactation cow that was genotyped as a heifer. Upon classification, the reliability of this animal’s Conformation index will increase from 68% to 75%. Once a lactation is completed, the reliability of her production index will increase from 73% to 78%. Despite the jump in reliability achieved by genotyping, the incorporation of performance data boosts the reliability, making the cow’s evaluation indexes even more accurate by approximately 10%. (Read more: Three Reasons Why Performance Data Will Always Be Important for Genetic Improvement)

Where does that data come from?

One of the more pertinent questions I hear being asked more frequently is, do we need to use official milk recording and type classification systems in order to validate this data?

With the introduction of on-farm computer systems, many breeders are not finding it necessary to use official DHIA milk recording systems.  That means instead of doing bi-weekly or monthly or sporadic tests for production, components and Somatic Cell Score, breeders who use Robots, for example, get this information with every milking.  This is a far more accurate way to measure production values. Instead of using algorithms to merely predict the in-between production data, these systems are working with the actual numbers.  In fact, these systems are such a complete herd management tool, `that they have metrics and information on many areas the current systems cannot even begin to predict. (Read more: The Future of Dairy Cattle Breeding Is in the Data, and Forget Genomics– Epigenomonics & Nutrigenomics are the future)

In speaking with many of the principal suppliers  in the robotic milking marketplace, they  often comment on that  the dairy breeding industry not only could have more accurate information, but  could also add indexes for more directly applicable evaluations such as feed efficiency.  While many organizations are trying to present algorithms to predict this measure, we could actually have performance data, which would significantly accelerate the accuracy and the rate of genetic gain in this core profitability area.

I have often heard the opposing argument from supporters of the current system. They cite that, since these numbers are not validated or conducted by a non-biased third party, how accurate can they be?  I find this argument doesn’t have any weight at all.   I have seen many hot house herds which have been able to “skew” the current numbers when they needed to. The argument that a third party verifies things means nothing.   With the fact that most new systems are computer based, there is actually the potential to implement a much more secure system for data integrity than the current process allows.  So really, the case for mandatory use of DHIA records is actually allowing far greater inaccuracy of the system, than if we accepted more modern computerized methods.

What about type classification?

The argument for the need for type classification is slightly different.  Since there is no computerized system to score a cow or to measure a cow’s conformation, there is no second data set that could be used instead of classification. Or is there?

Type classification was created in order to predict a cow’s longevity.  Isn’t that exactly what herd life and productive life measure?  Moreover, instead of being based on a prediction, they are  rooted in 100% accurate longevity data.  (Read more: Is Type Classification Still Important?,  She Ain’t Pretty – She Just Milks That Way! and Does Classifying Excellent Mean Profitable? Now? In The Future?)

Hence, the argument for the need to validate conformation data through classification is missing the boat.  Instead of trying to hold on to a system rooted in the past, we should embrace the more relevant data and information available. We should change the systems to evaluate genetic progress and merit based on actual information and should not continue to rely on a subjective system which tries to make predictions. The actual information is available.

What About Registration?

On-farm systems are such an accurate and efficient way to record breeding, calving and parenting information that the arm’s length breed association registration is duplication. Genomic testing provides 100% verification of parentage. (Read more: What is the Role of a Dairy Cattle Breed Association?)

The Bullvine Bottom Line

And so we see that the arguments supporting the need to continue type classification, milk recording and registry are becoming redundant.  Instead of trying to keep a system that validates old school genetic evaluation systems that are based on trying to use algorithms to predict genetic merit, we should be embracing the wealth of new and more accurate information that is available. We should be creating a new system that is based on measurable profitability and herd improvement statistics. The only reason that is left for keeping these three expensive programs is because we feel a need to validate an old animal model.  Instead, we should be creating a new animal model. One that accurately reflects the way modern dairy farmers operate.

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

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Go to any purebred dairy cattle sale and listen to the pedigree person. What are they saying? Usually is an exhortation to buy the animal in the ring because it has a gTPI of 2700 or her dam was Grand Champion at prominent show or she comes from eight generation of Excellent dams.  In essence what we are being told is that this animal is at the top of the breed and you should buy it. So does dairy cattle breeding work by identifying one number, one show or one family and only using that information to make decisions on. I think we all know the answer to that question … and the answer is…. “NO”! But let’s step back and, regardless of a breeder’s focus, look at how the understanding of all the numbers could be simplified when it comes to genetic information on sires.

The Information We See

Three times a year after each index run, breeders are bombarded with fliers, proof sheets, and fancy sire catalogues with numbers, numbers, numbers and cover girl like photos that make you wonder why the classifier only made the pictured first lactation cow GP 80. Was the classifier blind? Is the photo an accurate depiction of the cow? Maybe The Bullvine is right about photo ethics (Read more: Dairy Cattle Photography: Do You Really Think I am That Stupid?, Dairy Cattle Photography – Over Exposed, Introducing the Dairy Marketing Code of Conduct).

But let’s get back to the numbers, numbers for sires.

So many of them. Often expressed differently. What is good and what is not so good? What’s this thing about a base roll on December 2nd and what does it mean for dairy cattle breeders? Why oh why can’t the brainy folks who compile the numbers make them so breeders can quickly look at a number for a proven or genomic bull and know if he is a standout, middle of the road, an also ran or an out-and-out loser. Don’t the genetic types know that bottom-line focused milk producers want quick and simple answers on bull rankings as they plant and harvest crops, handle manure, feed and manage cows, coach 4-H or FFA and yes, educate their children.

What is #1? Does it Matter?

However at the same time that milk producers are asking for simplification, many breeders are striving to have Mr #1 Sire. First it was 2500 gTPI and now it is 2700 gTPI. Or first it was 1000 NM$ and now it is 1150 NM$. Can the difference between 2600 and 2700 gTPI be quantified when it comes to mating cows? If a breeder has a cow that needs improvement in protein yield and feet and legs which sire should he use? Is a sire with 39 lbs of protein and 1.81 for Feet & Legs Composite good enough? Bottom line focused breeders need a universally expressed number for all traits so they can say to their genetic advisor whether to include a sire in the mating program. Of course having a breeding plan that includes needs and priorities is needed for a mating program to be successful. (Read more: What’s the plan?)

Percent is Universal

Every student is trained to understand that 100% is the best mark possible, 75% shows good proficiency and 50% is just a passing grade. So why couldn’t the same thing apply to genetic evaluation results? That way breeders would not need to know what is the very best value, how to distinguish if this is on the new or old base or where a sires daughters are inferior.

Breeders Want to Know

Breeders do not want to carry several files on their electronic device on what is top, good, okay or bad for each trait. All they want to know for the sire they are looking at is – what are his strengths and weaknesses relative to his contemporaries?

Breeders expect their nutritional advisors to know the fine details about balancing rations. As well they expect their genetic advisors to know all about how to improve their cows and herd from a genetic perspective. In both cases breeders expect their advisors to use the KISS principle – Keep It Simple Stupid. (Read more: gPs– Genetic Profile Systems – Dairy Cattle Breeding Made Simple)

Does This Fit Breeders Needs?

The following charts are provided so Bullvine readers can consider if breeding the females in their herds would be easier for them if sire indexes were expressed on a percent basis. A percentage of what the very best contemporary’s index is.

Table 1 – Top Ten gTPI Daughter Proven Sires (Aug ’14) Expressed as a Percent*

Segment#Avg. LPIAvg. Sale PricePrice/LPI Point
>3000LPI803286$60,021 $18.26
>2000 LPI <30001642589$16,384 $6.51
<2000 LPI561637$8,879 $5.42
R&W262093$24,600 $11.75
Polled262275$37,076 $16.30
Show Heifers or All-Canadian Pedigree522005$17,154 $8.56

* Percent of the index for the #1 sire for the trait within the category

A quick review of Table 1 shows:

  • Facebook achieves the #1 position based on his high production and good type classification conformation
  • Dorcy, AltaGreatness and Large daughters have the udders
  • AltaGreatness, AltaFairway and Junior are below average compared to their marketed contemporaries for Feet & Legs
  • As a group all these sires can be expected to produce daughters that are very high for gTPI
  • Breeding on gTPI only will miss the fact that sires have strengths and limitations
  • Using only the top gTPI sires is not likely to produce show winners

Table 2 – Top Ten gTPI Genomic Sires (Aug ’14) Expressed as a Percent*

RANKNAME# OF DAUGHTERSPTATUdder CompF&L CompBody CompDairy CompStature
1BRAEDALE GOLDWYN553.032.592.561.932.033.1
2REGANCREST ELTON DURHAM-ET212.472.312.131.71.982.13
4REGANCREST DUNDEE-ET182.062.180.751.291.551.18
5GEN-MARK STMATIC SANCHEZ143.072.172.443.342.833.91
6WILCOXVIEW JASPER-ET112.891.940.732.562.523.22
7MAPLE-DOWNS-I G W ATWOOD-ET84.163.413.463.442.974.31
9PICSTON SHOTTLE-ET62.661.971.792.422.32.71
9ROYLANE JORDAN-ET62.071.940.321.532.061.93

* Percent of the index for the #1 sire for the trait within the category

A quick review of Table 2 shows:

  • Very little separates #1 and #10 on the list. Remember that genomic bulls are 70% Rel.
  • Within individual traits there is considerable variation among these sires
  • The percentages identify that every sire has one or more limiting factors
  • As is always recommended use several genomic sires instead of one or two
  • Supershot, Delicious Coin, Delta and Rubicon are high for production
  • Alta1stClass, Kingboy and Monterey stand out for conformation

Table 3- Top Ten NM$ Daughter Proven Sires (Aug ’14) Expressed as a Percent*

Segment#Avg. LPIAvg. Sale PricePrice/LPI Point
>2000 LPI <30001642589$16,384$6.51
<2000 LPI561637$8,879$5.42
Show Heifers or All-Canadian Pedigree522005$17,154$8.56

* Percent of the index for the #1 sire for the trait within the category

A quick review of Table 3 shows:

  • The vast majority of these sires will have daughters that produce high volumes of fat and protein
  • Yano, Erdman, Marian944 and Twist stand out for Productive Life
  • Robust is in a league all his own for Daughter Calving Ease
  • Twist claims #3 position on NM$ and has high PL, SCS and DPR.
  • SCS needs to be interpreted carefully as sires with poor SCS are not returned to active service

Table 4 – Top Ten NM$ Genomic Sire (Aug ’14) Expressed as a Percent*

Segment#Avg. LPIAvg. Sale Price

* Percent of the index for the #1 sire for the trait within the category

A quick review of Table 4 shows:

  • Percentages make it quick and easy to identify both strengths and limitations for a sire
  • Delta, Supershot and Dozer do not have significant limitations
  • Eight of the sires have over 80% for Productive Life
  • SCS, DPR and DCE percentages vary quite a bit but that’s to be expected for sires that do not have milking daughters

The Bullvine Bottom Line

Understanding index values is important but having multiple ways of expressing the results of genetic evaluations can result in breeders saying “Too much information. Give it to me in terms I can quickly comprehend”. Being a good dairy farmer requires that managers know a great deal about many disciplines. A good dairy farmer understands that effective breeding requires equal parts art (cow sense) and science (number crunching). Simplifying the expression of genetic evaluation results could be a step forward for all breeders.

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





There is an old saying about “Keeping up with the Joneses”. The term is often attached to things that happen in high society, but it can also be attached to the purchase of material things. Three decades ago it was installing a home swimming pool. Ten to fifteen years ago it was making sure that your children were introduced to the use of a computer. Recently it has been joining Facebook? Well, dairy cattle breeding is not exempt from change.  Today The Bullvine wishes to overview and provide some comments about keeping up with the changes in genetic indexes for December 2014 recently announced by the Council On Dairy Cattle Breeding (CDCB). For readers interested in exact details, they can go to

Weekly Genomic Evaluations

The first thing to take note of is that genomic indexes will be available every Tuesday (8 am Eastern Time) for animals that have had their analysis completed in the past week.  These weekly released indexes will be approximate as they will not be a full run of the evaluation system. Then once a month the full evaluation will be done and released on the first Tuesday of the month. Some breeders will ask ‘Why do an approximation? Just release the results monthly’.  There are two reasons for this move: 1) The work flow at the analysis lab can be evened out throughout the month; and 2) Breeders can select, sell or cull animals (or embryos) earlier thereby minimizing the expense of raising calves.

Be Clear About the Release Date

For buyers, using genomic evaluation results, it will be important that they ask for the date of release of the results.  It is entirely likely that this change to weekly genomic releases will create confusion until breeders are aware that weekly releases are approximations and until CDCB irons out any wrinkles there may be at the start. As well buyers interested in knowing how close to the top of an elite list that an animal is will need to do extra checking. I think we all knew that in time there would be more and more frequent reporting of animal’s genetic indexes. Dairy cattle breeding is faster every year that’s what happens when genetic advancement is rapid. Breeders need to make sure that they ask if an animal tops the list at the time of the official releases in Dec, April or August, or at the time of the nine other monthly releases, or on a weekly release.  Make sure you ask for the release date.

Base Roll

Every five years the base to which all animals are compared is updated. In December, the base will change to all cows born in 2010 from all cows born in 2005. On the CDCB website, the changes for all traits and all breeds are listed. Table 1 lists are some of the changes in indexes breeders can expect for Holsteins and Jerseys both of which have made significant genetic improvement from 2005 to 2010.

Table 1 – Index Changes That Will Occur in December 2014

Holstein Jersey
Net Merit $ -184 -124
Protein (lbs) -12 -12
Fat (lbs) -17 -19
Milk (lbs) -382 -327
Productive Life (months) -1 -0.8
SCS 0.07 -0.04
DPR -0.2 0
CE 0.4 n/a
DCE 1.6 n/a
UDC -0.92 -0.33
FLC -0.78 -0.15
BDC -0.61 -0.15
Final Score -0.99 -0.53

Breeders can expect that bulls and cows will have their genetic indexes lowered.  The relative rank of animals, of course, will not change. All animals will be affected to the same degree. Bulls that were $700 NM will now be $516 NM.  A base change time is an excellent time for breeders to re-evaluate the minimum values they will require bulls or replacement females to meet.

NM$ Index

Based on the up-to-date facts on genetic merit of the USA dairy populations and the economics of dairy farming in the USA, researchers at USDA-AIPL have fine-tuned the Net Merit index formula. Table 2 provides a comparison of the traits included and their weights for the formula used from 2010 to 2014 and the new formula for 2015.

Table 2 – Traits and Weights * in NM$

2010 2015**
Milk 0 -1
Fat 19 22
Protein 16 20
PL 22 19
SCS -10 -7
UDC 7 8
FLC 4 3
BDC -6 -5
DPR 11 7
CCR 0 2
HCR 0 1
CA$ 5 5

* A negative value indicates that a higher rated animal impacts negatively on NM$
** Indexes that will be issued on December 02, 2014

The changes may not seem major, but it should be noted that the emphasis on production traits are increasing from 35% to 43%.  This is similar to the change in emphasis that will occur in TPI in December (link to MSH’s article on changes for TPI). Breeders can expect that there will be re-ranking of bulls for NM$ especially for bulls that either excel or are below average for their production traits indexes. Animals that excelled for SCS, PL and DPR, can be expected to fall back relative to other animals in the breeding population. Breeders should take time to go through the new rankings in December before ordering semen, purchasing embryos or replacement females.

A New Grazing Index

Based on breeder requests, CDCB will be producing a fourth total merit index called Grazing Merit (GM$). The three previous total merit indexes, Net, Cheese and Fluid will remain in place. GM$ will take into account the needs of grazing herds and reflect the need in those herds for high fertility and seasonal calving cycles. With the move, in some regions or countries, to have the cows harvest their own forage and the production of milk during the growing season, this index is sure to get serious consideration.

Fertility Indexes

As noted in Table 2 heifer and cow conception rate genetic indexes are now included in the NM$ formula. The rationale is, of course that a conception must take place before there is a pregnancy. Fertility will no longer be solely DPR. As well the methodology for determining DPR will change with more information incorporated into the calculation. Breeders can expect that for some sires, there may be changes in their DPR as the correlation between the previous and the December DPR proofs is only 0.97.

New Genetic Evaluation Software

The new software has been used for calculating all fertility indexes since December 2013. This change in software will not be as obvious to breeders. The software in use previously was implemented in 1989. Since then, computational strategies and methodologies have been significantly enhanced. Extensive comparisons have shown that, for the daughter proven sires, the correlation between the evaluation results for the new and old software is 0.995. That is very high. However for cows and genomically and parent average evaluated animals, there may be some changes due to a software change.

Sign Up to Learn More

Holstein USA wants all breeders, regardless of which breeds they have in their herd, to have the latest details before December 02.  They will be doing that by hosting a webinar on November 13 at 1 pm Eastern Time.  Details on the webinar can be found by going to and on the home page will be found a link to the webinar. Click on the link – people wishing to participate in the webinar will need to register.  Interested people should register early.

The Bullvine Bottom Line

It is recommended that breeders take the time after the indexes are released on December 02 to go through the official listings with the goal of objectively selecting the animals, especially sires, which best meet their breeding plan. (Read more: What’s the plan?). We say objectively because it could well be that a sire you were using this fall no longer ranks high enough for you to continue to use him. However, it is not only sires that we must be objective about. Some previously high donor females may also drop. However, there will also be animals that go up in their rank position in their breed.

Even though our first reaction may be to say that the new index is wrong, we must remember that the researchers have worked hard to bring the industry more accurate information so dairy breeders can continue to move their herds forward genetically — as rapidly as possible! Making it possible to keep up with the Joneses!!



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For the 1% of breeders who deal in seed stock Proof Days are like Christmas 3x times a year.  But for the remaining 99% of dairy breeders proof days, the days when the latest Genetic Evaluations are released, are not that big a deal.  But they should be.

The following are three reasons all dairy producers should be checking out the latest genetic evaluations.

All producers should be using the best genetics possible

Analysis conducted as a cooperative effort between Canadian Dairy Network (CDN) and the milk-recording agency in Québec, Valacta, examined the association between the average profit per cow at the herd level and the genetic potential of the herd for various traits.


Figure 1 shows the relationship between the average LPI and the average profit per cow per day in each herd studied. While there are some exceptions to the rule, the dark line in the graph reflects the average relationship across the LPI scale, which indicates that herds with higher average LPI levels of their cows also have higher profit values. This positive correlation between LPI and profit clearly shows that genetics is a significant contributing factor but that management also plays a major role. On average, for every 100-point difference in LPI at the herd level there is an increase in profit per cow per year of $50, which accumulates from year to year. From a sire selection perspective, this equivalence translates to a difference of $50 more profit per daughter per year for every 200-point difference in the sire’s LPI value.  Based on a 50% conception rate, that would indicate that the semen from a sire who is 400 LPI points higher than the average sire, should cost $50 more.  Applying this to the current sires available, by using a sire such as AltaRazor who has an LPI of +3038 you will generate and extra $187.50 compared to a sire with an LPI of 1500.  This is from direct daughter profitably and does not even factor in the increased performance of any progeny this cow would produce.  So then investing $50 to $100 more for semen that will deliver over $180 in return is certainly a profitable decision even for commercial milk producers.

The Grass Is Always Greener on the Other Side of the Fence

I often hear many producers quote the minimum levels for certain traits that they are willing to use.  The challenge with that is while this approach is great for setting basic criteria, it fails to look at how these sires compare to other sires.  By using “any” sire that meets their criteria they are missing out on maximizing the genetics gain, and therefore the profitability of their herd.  As demonstrated above setting a minimum threshold, instead of going for maximum return, is leaving dollars on the table, and not in the milk check.  Then there is the case where some milk producers prefer to deal with only one semen sales representative or A.I. company.  No A.I. company has all the best sires (Read more: Stud Wars: Episode II – April 2014), so by employing this practices any savings or efficiencies you gain from negations, are negated by the amount you are costing yourself in loss of genetic potential.  (Read more: Rumors, Lies, and other stuff Salesmen will tell you and Are There Too Many Semen Salesmen Coming In The Lane?)

Are You Sure You Are Getting What You Pay For?

With the latest reports indicating that genomic young sire use is approaching 60% in North America, many producers have embraced genomics in a significant way (Read more: Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!).  I have even come across herds that have gone to 100% genomic young sire use.  With such a heavy usage of sires that are 60-70% reliable, are you sure that the sires that you are using are delivering on the other end?  A great way to check this is to see how the sires you are investing in, are doing when they receive their official daughter proof.  Sure that may not mean that you go back and use these sires once they are proven, but it does help you get a better understanding of the reliability of the genetics that you have invested in.

The Bullvine Bottom Line

I am not saying that all dairy producers should be waiting with baited breath at 8 am on proof day.  However, there is certainly value in taking the time to check out the latest sire evaluations, to see how the sires you have been using are performing and what other sires are out there that could help you increase the profitability of your herd.  No matter what your management style, there are certainly enough reasons for you to get excited on proof day.

Check out the latest Holstein Sires Proofs in our Genetics Section

The Dairy Breeders No BS Guide to Genomics


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Want to learn what it is and what it means to your breeding program?

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For over twenty years USDA-AIPL and now CDCB have been publishing Net Merit (NM$) values for dairy cattle with US genetic evaluations.  Over those twenty years five revisions have been made to the formula, the last in 2010, as new traits have been added, new genetic evaluation methodologies have been developed, and the economics of dairy farming has changed. The next change in the formula will occur in December 2014.

It is important that breeders consider the impact of the coming changes as they review the sire, cow and heifer NM$ indexes on August 12th.  Breeder consideration is needed because the matings that are made this fall will have offspring born in 2015 when the new formula will be in place. Obviously the changes in the formula will not affect how the new future animals will perform but it will, however, affect where the animal ranks for marketing purposes and where a herd’s genetic level for NM$ is relative to other herds.

Let’s dig deeper and see what changes are to take place and how that may affect current breed leading NM$ sires.

Significant Changes Coming In December

The following table compares the weightings, 2010 to 2014 (December), for the components of the NM$ formula.

TABLE 1: Comparison of Relative Emphasis for Traits in NM$ Index

DE-SU OBSERVER-ET16027.22.7667922.73.020.892332
HONEYCREST BOMBAY NIFTY-ET2367.22.627553-0.46-0.130.971810
POTTERS-FIELD KP LOOT-ET10047.22.6876500.081.71-0.241954
KELLERCREST BRET LANDSCAPE817.12.3685060.651.271.161838
WHITMAN O MAN AWESOME ANDY2026.92.5557540.32-0.171.212063
ZIMMERVIEW BRITT VARSITY-ET4106.82.6266680.71-0.471.552013
CLEAR-ECHO NIFTY TWIST-ET9426.82.628748-0.32-0.421.172039
KED OUTSIDE JEEVES-ET3556.82.83105151.370.971.741913
ENSENADA TABOO PLANET-ET22166.72.9867211.931.44-0.472176
GOLDEN-OAKS GUTHRIE-ET10786.72.786535-1.15-1.240.361728
DALE-PRIDE MANFRED ALFIE5196.62.966461-0.63-0.36-0.011702
LAESCHWAY JET BOWSER 2-ETN2006.52.8474551.622.031.831940
ELKENDALE DIE-CAST-ET-8726.52.7263700.681.851.991718
LAESCHWAY JET BOWSER-ET2006.52.8474551.622.031.831940
BADGER-BLUFF FANNY FREDDIE12366.42.757791.571.62.872292
CABHI AUSTIN POTTER-ET1516.42.8165200.050.410.021766
CABHI MOOSE-ET456.42.6463730.180.31.111625
SILDAHL JETT AIR-ET11186.32.6466442.882.262.912168
SPRING-RUN CAMDEN-676.22.9174330.571.790.61762
KERNDT MAXIE GOLDSTAR-ET1996.22.576449-1.28-0.61-0.961631

Thoughts on the changes include:

3 Proven Sires Favored by New Formula

Three currently (April 2014) high NM$ proven sires will gain from the new formula. They are: Roylane Socra Robust; Den-K AltaGreatest; and Mainstream Manifold. They are all high production sires, and the new formula will favour them. All three, Robust, AltaGreatest and Manifold will also benefit from less emphasis on their average traits – SCS and DPR.

Breeders can expect to see sires that have production indexes below 1500 lbs for milk and 65 lbs for fat drop relative to other sires for NM$. Sires over 2200lbs milk, 80 lbs fat and 55 lbs for protein will rank higher for NM$ come December 2014. Breeders that use NM$ in sire selection should consider discontinue using, after August 12th, sires with low production indexes.

2 Genomic Sires Going Up!

Two currently (April 2014) high NM$ genomic sires will be rated higher with the new formula. They are: Cogent Supershot; and Uecker Supersire Josuper. They are outstanding for production. Supershot – 2528 lbs milk, 100 lbs fat and 85 lbs protein. Josuper – 2971 lbs milk, 118 lbs fat and 92 lbs protein. Supershot has good ratings for the other traits so will remain to standout for NM$. Josuper will benefit from less emphasis on traits where he is breed average.

Many current relatively high ranked NMS genomic sires will fall back if they have only moderate milk indexes.  Breeders should consider discontinuing the use of genomically evaluated sires below 1600 lbs milk, 85 lbs fat and 60 lbs protein.

The Effect on Polled Sires

Current marketed polled proven sires are not highly rated for production, so will not fair well with the new NM$ formula. On the genomic sire side, two high production sires standout as sires that should increase in their relative NM$. They are Bryhill Socrates P (1914 milk 99 fat and 65 protein) and Pine-Tree Ohio Style P (2033 milk, 64 fat and 57 protein). Other sires that will do relatively well under the new NM$ formula are Kerndtway Eraser P, Da-So-Burn MOM Earnhardt P and Pine-Tree Ohare P.  Many polled sires have below 1000 lbs of milk and can be expected to drop significantly in NM$ come December.

1 Star Sires of Sons

One sire of sons stands out as benefiting, in a significant way, from the new NM$ formula. That sire is Seagull Bay Supersire. His high production numbers put him in an elite status – 2434 lbs milk, 111 lbs fat and 78 lbs protein. The reduced emphasis on SCS and DPR, in the new formula, will also help Supersire, as he is average for those traits.

Other genomically evaluated sires of sons, heavily used over the past couple of years, often have been only moderately high for production traits. Included in this category are sires such as Mountfield SSI Dcy Mogul, De-Su BKM Mccutchen and Amighetti Numero Uno. These sires do have some outlier high production rated sons but, on average, the majority of their sons will drop for NM$ come December.

Be Prepared to Avoid Inbreeding

With both Robust (sire) and Supersire (son) in heavy use and both benefiting from the new NM$ formula, it will require that top outcross sire and female lines be identified and used in order to avoid inbreeding. That can be accomplished by breeders using both corrective mating and genomic testing.

The Bullvine Bottom Line

The changes coming for the NM$ formula in December 2014 are not just minor tweaks. Breeders that use the NM$ index in sire selection should be prepared to set aside sires that in the past have had high NM$ ratings but were only average to slightly above average for their production indexes.

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





Dairy farmers want to avoid mastitis. It’s expensive – antibiotics, lost milk, extra staff time and lost genetics. Furthermore every dairy operations targets to have the food safety and milk product quality that consumers want and deserve. When SCC testing through DHI and subsequently SCC sire proofs became available significant improvement tools were available to dairy cattle breeders. Breeders knew from experience that some cows and cows families were more prone to getting mastitis. Although somatic cell information was a great first step, it wasn’t the total answer. Breeders questioned if SCC could be too low and if very low SCC cows actually have less ability to fight off infectious agents that cause mastitis. So breeders asked the researchers to investigate further.

Canadian Stats Lead to First Mastitis Resistance Ratings

At CDN, breeders and researchers put their heads together in 2007 and decided to ask breeders to report on eight cow health events (Read more: Is Animal Health Important to You?) to get the necessary field information on incidences. For more than five years, 40% of Canadian milk recorded herds have been reporting if a cow has had mastitis and any of the other seven health diseases since her last test day. That information plus her somatic cell scores and genomic profile were combined to develop animal genetic ratings for mastitis resistance that will be released for the first time by CDN (Read more: Mastitis Resistance Selection: Now a Reality!) on August 12, 2014. By using the negative of a mastitis case plus the actual facts on SCC and genomic profile, a new tool will be in the hands of breeders to use in making their selection decisions.

The study of the data collected showed that Mastitis Resistance has a heritability of 12%, similar to the heritability of an important trait like feet and legs and therefore it is possible to improve it genetically. As many discerning breeders suspected, the study showed only a moderate association between a positive genetic rating for SCC and incidence of clinical mastitis in first lactations (44%) and later lactations (58%). SCC genetic indexes are an indication of few mastitis cases but a considerable distance from the accuracy breeders expect.

Mastitis Resistance Sire Proofs

After developing the formula calculating genetic evaluations for mastitis resistance, CDN researchers then compared the results to existing known facts. It was found that Sire Proofs for SCC have a correlation of 80% with Sire Proofs for Mastitis Resistance. That is moderately high but not perfect. And Sire Proofs for Mastitis Resistance were strongly associated with incidence of mastitis in first lactations (85%) and later lactations (90%). Note that the associations for first and later lactations are closer for Mastitis Resistance than they are for SCC.

When CDN publishes the genetic indexes in August, the scale will be 100 for average with a standard deviation of +/- 5. The following table produced by CDN is very interesting.

Source: Mastitis Resistance Selection: Now a Reality! CDN July 2014

Source: Mastitis Resistance Selection:
Now a Reality! CDN July 2014

This table provides for breeders some information details for both clinical mastitis (actual mastitis cases) and sub-clinical mastitis (SCC).  On a population wide basis breed average bulls (100) for Mastitis Resistance will have 92% healthy daughters with an average SCC of 178,000 in their first lactation.  In later lactations an average bull will have 88% healthy and an SCC of 226,000 in second lactation and 292,000 in third lactation. It should be noted that if a bull is used that only has a 91 rating, breeders can expect his third lactation daughters to average 400,000 SCC. In many countries 400,000 is now, or soon will be, the maximum allowable for milk to be accepted for shipment off-farm. As mentioned the numbers in this table are for an average herd. Individual breeders with less mastitis incidence can expect healthier animals and lower SCC average. However herds, with higher than average mastitis incidence, can expect poorer results.

In August Mastitis Resistance sire proofs will be published by CDN for Ayrshire, Holstein and Jersey breeds. Due to the large number of Holstein bulls with proofs and genomic profiles, CDN will publish genomic evaluations for Mastitis Resistance for the Holstein breed.

The Bullvine Bottom Line

CDN Mastitis Resistance genetic indexes will increase the accuracy of selecting animals for their ability to avoid the significant cost of udder disease. It is the tool that breeders have been asking for. It came about when breeders, researchers and genetic evaluation officials collaborated. Look for bulls or cows that are 105 or higher before considering them to be significant breed improvers.




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Dairy breeders are continually taking steps to be more exact about the way they farm and the products they buy, produce and sell.  However when it comes to the genetic make-up of our animals there remains significant difference of thought, amongst breeders, about the actual accuracy of the genetic information. Breeders are presented with a wide range of facts. Gold Medal, Extra, Star Brood, DOM, proven, genomic, photos, Supreme Champion … no wonder many breeders are confused. The Bullvine feels that breeders need to be objective about the animal information they see and to think in terms of the accuracy of the information. Now we are not talking about whether or not an animal meets the ideal. We’re talking about how much we can rely on the facts we see in hard copy or from virtual communication sources.

In the Beginning

In the nineteenth century milk cows were mostly dual purpose and herd size was small. People wanting to get into dairying purchased a cow or bull based on what the seller said were the animal’s merits. In time breed societies were formed to document lineage. That was followed in the early twentieth century with third party authentication of both yield and conformation.  The third party oversight of parentage and performance were the beginning steps to know the accuracy of the information. That was the start.

Many Steps Along The Way

Having a milk record or type classification authenticated for a single one cow in a herd was initially thought to be very useful information. The next move was to compare a cow to her dam to see if improvement had been made.  But that did not help much as the cow and her dam were not simultaneously at the same age and, in some cases, not in the same herd. Of course, over time we have learned that we need to know the performance of the cow’s herdmates. That was the stage where breeders started to compare animals within a herd with the desire to know which animals were superior, or, conversely, inferior for a trait. The biggest breakthrough in accurately determining the relative genetic merit of an animal came when Dr Charles Henderson, Cornell University, developed the analysis technique that he called B.L.U.P. (Best Linear Unbiased Prediction).  Forget about trying to understand the term, what it does is compare all animals within a herd and then compile the results across all herds to produce genetic rankings for males and females.

What About Accuracy?

From a genetic merit perspective it is important to know two things. Firstly where does the animal rank in the populations? And secondly, and also very important, how accurate is the prediction? How much trust can a breeder put in the animal’s genetic rating? If information is of limited accuracy, then it may be nice to know, but it does little for constructive breeding or to provide the opportunity to drive up on-farm profits. Accuracy produces confidence; confidence accelerates advancement, and negligence ruins the reputation which accuracy had raised. (Read more: Has Genomics Knocked Out Hot House Herds? And The Hot House Effect on Sire Sampling)

Let’s Compare Accuracy

The range in accuracy of genetic evaluation indexes goes from 0 to 99% and is called Reliability. The following chart is an approximation of the accuracy of predicting an animal’s total merit index (i.e TPI, NM$, LPI, or any other national total merit index) from the information that is known on the animal.

Reliability In Predicting An Animal Total Merit Index

Genetic Accuracy – Can you trust the numbers2

As far as accuracy goes the winners, as a result of incorporating genomic information into our genetic evaluation systems, have been young bulls, young heifers and brood cows. Adding genomic information has resulted in a doubling of the accuracy of their indexes. For further information on accuracy an interesting read is Two Ways to Look at Accuracy for Genomic Young Bulls published by Canadian Dairy Network.

What’s Ahead?

As more and more animals are genomically tested and recorded for their performance, the accuracy of all genetic indexes will increase.  Three other steps that will assist in increasing the accuracy of total merit indexing are needed:

  1. Have every milk weight, fat %, protein% and SCC automatically captured at every milking;
  2. Have information on new economically important traits collected;  and
  3. Have more economic information available on more traits.

Breeders will be the benefactors of having more and more accurate information so that they can make more and more accurate decisions.

The Bullvine Bottom Line

Having genomic information has been a significant step forward for increasing the accuracy of genetic indexes. But it will go beyond genetics and genomics in the future. Read past Bullvine articles for further details about genomics for health and management (Read more: Herd Health, Management, Genetics and Pilot Projects: A Closer Look at ZOETIS) and what lies beyond genomics (Read more: Forget Genomics – Epigenomics & Nutrigenomics are the Future). When buying genetics breeders need to check that the animals, semen or embryos they are considering will both follow their breeding plans (Read more: What’s the plan?) and that the information is accurate.  Breeding dairy cattle is faster paced every year. The accuracy of the information used is an important consideration.



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From when to plant, fertilize or harvest our crops to what sire to use, breeders are always looking for reliable assistance.  For most dairy farmers, there are two things they love to complain about.  One is the weather and the other is bull proofs.  No one ever says that predicting the future is easy.  Sure we put more credibility into Al Roker’s weather forecast than we do the one given by the young blonde, who seems to be there more for eye candy than for knowledge set.  But the question remains, “How accurate is either weather forecast?”  At the Bullvine we decided to look at how the genetic evaluations system compares to the predictions of meteorologists.

In many ways Dairy Cattle Genetics and Meteorology are very similar.  Both use complex mathematical models to predict the future.  The formulas and complexity of these models make most people’s heads spin.  But after all the numbers and formulas are calculated, who does the better job?

To compare these two prognosticators we looked at the accuracy of the average 3 day weather forecast from the National Weather Service last year and compared them to  initial genomic proofs of young sires and then to  a bull’s  first daughter proofs.  What we found was that the average 3-day weather forecast is accurate, within e degrees, 71.19% of the time.  For genomic young sires, we know that the average sire with a 50K test compared to a proven sire is about 72% reliable.  So the average young sire’s proof is as accurate as a 3-day weather forecast.  Sure things can change quickly but more than 70% of the time you can rely on the information to be accurate and 95% of the time you can expect a genomic tested young sire to perform at least within 20% of their expected values.  (Read more: The Truth About Genomic Indexes – “show me” that they work!)

When comparing a next day forecast to that of a 1st crop proven sire, we find the advantage for accuracy goes to the geneticists.  The next day weather forecasts for the national weather service’s jump up to 87.24% accurate to within 3 degrees, and 1st crop proven sires with a genomic test are 90% accurate.  To put things into perspective.  A non-genomic tested young sire’s proof is as about as accurate as a 7 day weather forecast.  Both are well below 50% accuracy and are more or less only good enough to forecast a general trend.

The Bullvine Bottom Line

Sure there are those who prefer not to use genomic young sires, when it comes to their breeding programs.  However I would hazard a guess that they are also using the Farmers’ Almanac, instead of the weather forecasts, to predict when to plant their corn or harvest their hay.  (Read more: Dairy Breeders vs. Genetic Corporations: Who are the True Master Breeders?)  For those breeders that are willing to let a little science help them to make their job easier, genomic proofs have considerably improved the accuracy.  Today’s average genomic young sire is about as accurate a prediction of performance as a 3-day weather forecast.  Accurate enough to make informed decisions, but not able to guarantee that a freak storm won’t come in and change things.



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Recently there has been a lot of discussion about the future of the dairy breeding industry.  New technology, new information and new organizations are entering the industry at record rates.  The problem is that along with all the changes there is also concern about who is leading these changes and protecting the interests of the average breeder.  One of the ongoing battles is the one surrounding the production and publication of US genetic evaluations.  The recent development of the Council for Dairy Cattle Breeding (CDCB) has sparked a war between CDCB and Holstein USA over access to information.  Both sides are threatening to take their toys and go home.

”He who controls the information controls the world.”

Is anyone even considering the answer to the question, “Who does the information belong to?”  As we wrote back in March of 2012 the conflict is over who will have control of the information.  (Read more: Council on Dairy Cattle Breeding: Land of the Free and Home of the Brave?) Now more than 2 years later this battle is coming to a head.  Rumors suggest that Holstein USA is threatening that they won’t share type data with CDCB/USDA because they are not in support of positions and actions being taken at CDCB and are even considering producing their own genetic evaluations for production in addition to the evaluations they currently do for type.  Now let’s be clear.  Up until this point Holstein USA has cooperated fully in the exchange of data.  However, they have been very upfront about their concerns regarding material licensing agreements (MLAs) and the usage of Holstein data.

Enemy at the gates

When you consider that larger and larger corporations have now started to enter into the dairy genetics marketplace, whoever has access to the information will have the power.  If these new players get instant free access to this information, what does that mean to breeders?  I would guess that it would not be positive to seed stock producers or to those who market and sell dairy cattle genetics that has already seen significant decline in their animal values.(Read more: An Insider’s Guide to What Sells at the Big Dairy Cattle Auctions 2013, Who Killed The Market For Good Dairy Cattle? and Is There Still Going To Be A Market For Purebred Dairy Cattle In 10 Years?)  You see the big nasty label should not be applied to the AI companies but rather to multinational supply companies.  That is the enemy I think the large AI companies are most threatened by.  Not the smaller AI organizations taking market share but rather these significantly larger corporations that have the resources to squash the large AI companies like a bug.

Imperfect Track Record

Now let’s say that USDA’s recent track record leaves some questions in many breeders’ minds.  Their decision to restrict breeders’ rights to genomic test their own bulls for a period of time certainly raised the ire of many.  Now the heated debate includes the formation of CDCB comprised of Breeds, DHI and AI (each with 3 seats on the board).  There doesn’t appear to be any apparent savings and no intention to reduce the USDA budget as a result of this decision.  And with the makeup of the board, it is felt that it is controlled by NAAB and the large AI organizations.

Once again this has me asking who exactly controls the information.

Holstein USA has been very vocal about stating that they have their members’ best interests at heart.  I respect that.  However I also see the other viewpoint that points out that this is the same information that members have paid for and yet they don’t get free access to it as in other countries.  Moreover, the limited amount of information that they do get access to comes with additional charges.  In the US is costs $8US to register a calf, in Canada it costs $9 CDN to register a calf.  Considering the exchange values these are about the same expense.  Though in Canada all information is then made publicly available to all.  In the US everyone has to pay an additional $3US per animal in order to get that information. So does Holstein USA really have their members interests at heart?  Or are they driven by their own survival and pocket book?  This is why the relevance of breed associations and programs like type classification are becoming key issues for many breeders.  (Read more: What is the Role of a Dairy Cattle Breed Association? and She Ain’t Pretty – She Just Milks That Way!)

The Bullvine Bottom Line

Am I saying that I am in full support of CDCB’s actions?  No.  It seems to be heavily weighted against breeders and towards the interest of the larger AI companies.  I am most concerned that breeders have access to information.  As more and more AI companies get into owning  females and  developing  of their own bloodlines, the  very livelihood of  seed stock producers is threatened (Read more: Should A.I. Companies Own Females?, Why Good Business for AI Companies Can Mean Bad Business For Dairy Breeders, and What the Experts Won’t Tell You about the Future of the A.I. Industry).  So I understand why Holstein USA should be concerned.  The majority of the membership, and especially those at the board level, is made up of these very seed stock producers.  So if they were truly concerned about these breeders, why don’t them allow them access to all the information?  It’s not about control.  It’s about breeders’ success. Nobody wins if infighting prevents progress.



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There is no question that, when you are looking to breed the next great show cow or sire of show winners, you are hoping to get a high type outlier.  You want to get the animal that is the farthest as possible from being average.  Yet all of the indexes provided to most breeders are averages.  They do not show you a sire’s ability to produce outliers.  They tell you the sire’s average performance and the problem is most breeders don’t want to be average.

The easiest way to find outliers is to compare two sires for their daughters’ performance. Then identify those sires that have the greatest deviation from their average daughter. This is not to be confused with Type scores in the US that are expressed in Standard Deviations.  The best way to describe this is by an example.

Let’s say we have two bulls each with 10 daughters.  The following table shows their level of improvement for type across the 10 Daughters.


Both of these sires would have an average improvement of 12 points.  Hypothetically if this was the whole population of their daughters they both would get the same conformation score.  The problem is they are two very different sires and the numbers tell us that.  However these are not the numbers that most breeders get to see.

Looking closer we see that Bull A daughters have a range of 18 points while Bull B’s daughters only range 4 points.  Sure both bulls, on average, will perform the same but, when you are looking to breed for the extremes (such as AI companies are), or you are wanting to produce the most consistent results possible, you need to know these differences between bulls. (Read more:  Duds and Studs – Why you shouldn’t use the same sires as the AI units).  This is also the reason you will often see AI units using a sire of sons that is maybe not #1 on the list, but rather a few places lower.  That is because he has exhibited the ability to show the greatest range in his progeny.

These numbers that the average breeder would never see are actually available to as they don’t generally get published.  But geneticists at the AI companies look very carefully at them.  They are available in the US – at least for production information if you search for them on the Council On Dairy Cattle Breeding’s website. This number is expressed as Daughter Yield Deviation (DauDev).  Daughter deviation is how much a given daughters spread out from the mean.  So it is a strong indicator of how variable his daughters are relative to other sires.  When we look at the top 10 domestic proven sires for Milk Yield in the US we find the following


What you see here is that STOUDER JAYVEN on average will produce the greatest production improvement (+2860).

Now. Let’s say you are not wanting the average performance.  Instead you want to find that outlier that will give the potential for the greatest improvement.  For that you would actually use DE-SU 553 NOBLELAND.  That is because his daughters have the greatest DauDev (+3544) and his average predicted transmitting ability (+2705) meaning that he has the variable potential improvement of +6249. That is 418 points higher than JAYVEN (+5831).  On average JAYVEN will outperform NOBLELAND. But NOBLELAND is the most likely to give you the greatest outlier.  That is because there is 27% greater deviation in daughter performance compared to average performance in NOBLELAND’s daughters than JAYVEN’s.

For those of you that are looking for the most consistent performer, you actually want the sire that has the highest potential with a small daughter deviation.  In this case that would be MISTVALE MAC.  While he will not give you list toppers, he will give you the most consistent performance with the smallest range in daughter performance.

The Bullvine Bottom Line

When it comes to finding outliers, you ultimately need to know the sires that will give you the greatest deviation in his daughter performance combined with his predicted transmitting ability.  One of the things that made sires like Braedale GOLDWYN exceptional was not his performance average but rather his ability to breed outliers for type.  When you are making your next breeding decision, ask yourself “Am I looking for an outlier?”  Or “Do I want the best average performer?”

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





For years there has been great debate between dairy breeders and producers about what type of cow is the most profitable.  There are sound arguments on both sides of this issue.  However, developments arising from new indexes and analysis highlight that it’s not always the prettiest cow that milks the most over her lifetime.  To paraphrase the popular song, these cows prove that “She ain’t pretty, she just milks that way!”

Are show cows great lifetime milk producers?

We are all guilty of it.  We see the cows that win at World Dairy Expo, The Royal, Swiss Expo, and IDW and are amazed at their extreme size, capacity, and dairy strength. We look at them as the epitome of what the ideal cow looks like.  And it’s fair to say that the production level of these animals has greatly improved over the past 30 years.  However ask any commercial producer in a large free stall environment and they would tell you that these winners would not be the ideal cow for their operation or to maximize their revenues.  The very characteristics that make them great in the showring (their massive size especially) would limit their efficiency for these producers.  (Side note: With dropping sale prices show cows and especially high index cows are not bringing the same resale value as they once did – Read more:  An Insider’s Guide to What Sells at the Big Dairy Cattle Auctions 2013).

Now here at the Bullvine we like to deal in facts not hearsay.  So we took the top 10 animals from the Mature Cow Class at the 2013 Royal and here is what we found.  They average an amazing 95 points with a couple even going Excellent multiple times.  The scarier part is that they only average 2.5 complete lactations each, out of a possible 4, and just over 50,000 kgs of lifetime production.  With the winner of the class, having out of three lactations started only completed 2 by 7 years of age and produced under 48,000 lifetime.  Now some would say, “Yes that is because all the big producers are in the Lifetime Production Class.”  So we decided to take a look at that class as well.  Surprisingly this class averaged a slightly lower 94 points, and just over 3.5 completed lactations each, out of a possible 5, and 61,647 kgs.  of lifetime production.  Not exactly extreme for a class that is supposed to be the epitome of the breed.  However there was one strong exception in the class, STARBRITE LYSTER LYNDSAY, who at EX-96-3E, with 5 completed lactations and 84,282 kgs (185,808 lbs.) of lifetime production, certainly is a testament to longevity.  That is probably why she is a perennial contender and a huge fan favorite.

84,282 kgs (185,808 lbs.) of lifetime production,

Are high scoring 2 year olds good lifetime producers?

Then of course there is type classification and the true type model.  Believing in full disclosure, we here at the Bullvine are big fans of the type classification system (Probably because my father ran the Canadian Type Classification and Breed Improvement Program, for 18 years in the 70’s and 80’s) and have written many articles about it (Read more: TOM BYERS: “THAT’S CLASSIFIED!” and Is Type Classification Still Important?). But more and more we are beginning to question some of the long standing beliefs that we have had relating to type classification and longevity.

There is no doubt that the goal of the type classification system is to produce a long lasting profitable cow.  What is becoming more apparent is that what we believed it took to achieve that may not have been functionally correct.

Now it would not be fair to make a blanket statement like that, nor would it be Bullvine style, if we did not back that up with cold hard numbers and examples.  I cannot think of a better example than, GILLETTE E SMURF, the world record holder for lifetime production at 242,303 kgs (534,181 lbs) in 11 lactations.  (Read more:  World Records Are Not Only Set at the Olympics).  As a two-year-old Smurf scored GP-83, with Dairy Strength (82) and Feet & Legs (80).  These two the traits kept her from going VG.  What makes this surprising is those are the two exact traits that many believe are the greatest indicators of longevity.  Yet the greatest producing cow in the world was deemed to be lacking in those areas.  In fact it was not until 10th lactation and over 216,893 kgs of lifetime production that the classifier deemed that Smurf had enough strength (97) and sound enough legs (86) to make her an excellent cow.

GILLETTE E SMURF EX-91-2E-CAN 242303kgs (534181 lbs) of lifetime production

Now as we always say it is easy to find case by case examples.  But do the numbers hold up across multiple animals and larger groups?  We decided to look at all the VG-89-2yr olds from January 1st 2007 to December 31st 2010.  In that time there were 20 VG-89 1st lactation cows that have remained in Canada.  60% of them have gone on to classify Excellent, with the group now averaging 91 points.  The alarming part is that, as a group, they have completed on average 2 lactations each out of a possible 4, with lifetime production averaging 42,262 kgs.  In fact only 30% of them have even completed a 3rd lactation.  That percentage is even less than that of the mature cow class at this year’s Royal.  Achieving VG89 first lactation certainly is not a good predictor of lifetime production. In analyzing the US numbers we found similar results.

So what is a good predictor of lifetime production?

We all have in our mind what the ideal mature cow looks like.  For many pedigree breeders it’s a cow that looks like this. (Read more: The Perfect Holstein Cow)

Mature Cow - composite background

In taking that one step further, we also did a composite of what the perfect classification 2 year old would look like.

2year old - composite background

But in reality, as we have mentioned earlier in this article, these cows are not the epitome of lifetime production animals.  In fact they are not even bull mothers.  Currently the typical ideal high genomic 2 year old/bull mother looks like this.

genomic 2 year old - composite background

But in analyzing the numbers, especially productive life and herd life, the true ideal 2 year old should look something like this.

efficient 2 year old - composite background

First, let’s make one thing clear.  Unlike indexes like TPITM and LPI that try to predict lifetime production based on hypothesis and our understanding of what we think it takes to make a long lived productive cow, productive life (USA), and herd life (CAN)  measure actual longevity.  They measure how many months the cow actually is a productive member of the herd compared to herd mates.

This means that our long-accepted theories that a cow needed to have a wide muzzle, deep chest, and deep sweeping open rib in order to be a high lifetime producer are actually incorrect.  As we pointed out in Breeding for Longevity:  Don’t believe the hype – It’s more than just high type, the top 25 productive life proven sires in the Dec’13 genetic evaluations actually average only 0.52 for Dairy Character and 0.47 for Body Composite.

This actually makes sense.  When you look at the top two reasons given for non-dairy purposes sales, infertility and mastitis, they account for almost double (26.9%) the number of animals culled for production or conformation reasons (18.5%).  Basically we learn that, when it comes to predicting longevity, there are many contributing beyond conformation.

That is why it’s not surprising when we interviewed Don Bennink of North Florida Holsteins, a very commercial production oriented breeding program, type and conformation where not even on his list of selection requirements.  (Read more:  NORTH FLORIDA HOLSTEINS. Aggressive, Progressive and Profitable!!).  In fact if you really want to break down the numbers into the nuts and bolts simplicity, you would only look at two things.  In the US that would be pounds of milk production (with some allowance for %F) and productive life.  In Canada that would be kilograms of milk production and herd life.

So here at the Bullvine we like to complete the steps for you.  We looked at all the proven sires who are over 1250 lbs of milk and 5 for productive life.  The results were very telling. There were 40 sires that made this list, with the top 6 reading like a who’s who of top selling sires, Bookem, Freddie, Robust, AltaMeteor, Shamrock, and Observer.  Also it is interesting to note that these sires average 2.77 SCS, 6 CE, 1.33 PTAT, 1.23 UDC, 1.23 FL&C and 2026 TPI.

NameFinal ScoreOwner
COOKIECUTTER MOM HALO-ET88Cookiecutter Holsteins
MSWELCOME OBSERVER LAURI-ET88Welcome Stock Farm, LLC & Charles Van Wie
HY-NIC-HOL TRYOUT STAR88Ryan L. Lindenmeyer
GLORYLAND DELLA RAE-ET88David A Tait & Hood Holsteins
CLEAR-ECHO SUPER 2140-ET88Clear Echo Farm LLC
HARVUE ATWOOD FOX-ET88David Meade Hardesty, Jr.
WINDY-KNOLL-VIEW POCONOS-ET88James R. & Nina P. Burdette
WINDY-KNOLL-VIEW PERFECT-ET88James R. & Nina P. Burdette
SAVAGE-LEIGH MAZEY-RED-ET87James R. & Nina P. Burdette
BELLTONE GOLD STAR LEE IV-ET87Kevin Doeberiener,PierreBoulet & Michael Heath
SUPER-K FORTUNE BONITA87Valerie L. Greco & Ronald J. Mikulice
GEORGETOWN SAN LIMELIGHT87Chris & Stephanie George
MIL-R-MOR FANCY FABULOUS-ET87Sarah Elizabeth Sheehan
SILDAHL AWESOME-RED87Fred Schoenbachler
LAKE-EFFECT DUR WREN-ET87Jeffrey & Gayle Benedict
ROSE-EDGE B PASTA-ET87Ernest H Jr & Carol W Ambler
ROCK-N-HILL-II CRANBERRY87Michael & Chris McCullough
KIKO GABOR RAPTURE 68587R & P Kiko Family Farms, Ltd
QUIET-MAN ALEX LOVELY-ET87Buttke Dairy Enterprises
KIKO DAMION VINA 66387R & P Kiko Family Farms, Ltd
PARADISE-R AFS GRACE 459487Paradise Valley Farms, Inc.
OPSAL DESTRY MARCELLA-RED87Joshua, Joseph & Felicia Opsal
SRP DESTRY FROLIC-RED-ET87John P. & Rachael Holmgren
MS BLONDIN JASPER BELLE-ET87Brad Stockman & Adam G Johnson
WEST-LAKE SS WENDY-RED87West-Lake Holsteins
HARVUE HERSHEY MINT87John O. Hardesty & Sons
HARVUE BLITZ GLITZ87John O. Hardesty & Sons
HARVUE ATWOOD VIDA87David M. & Debra L. Hardesty
HOSTO SS HILLROBIN87Kelley L. & Ruth Ann Hosto
WHITELEATHER ALEXAND 169387Lauren G. Whiteleather
HOLMGREN TRIUMPHANT DI-ET87John P. & Rachael Holmgren
MS ANGELINA ANGASHOCK-ET87Claquato Farms Inc. & Robin-Hood Holsteins
SCH-GER ATWOOD ELYSE87Brett Morlock & Ken Gerber


Now for those of you who are wanting to push the genomic envelope, we did the same analysis, though factoring in the typical genomic over prediction of about 20% (Read more:  How Much Can You Trust Genomic Young Sires?).  Our requirements were 1,500 lbs of milk and 7.2 for productive life.

NameClassScoreSire NameOwner(s)PROV


The Bullvine Bottom Line

Any way you look at it, it’s hard to argue with the cold hard facts.  For years the show ring and type classification have tried to do the best job possible in predicting what it take to produce a long lived productive cow.  But just like the evolution of the computer, healthcare and science, as more information becomes available, we find that some of our previous beliefs are no longer accurate.  In no way am I saying that there is not value in programs like type classification, it is just time for those programs to evolve and do a more accurate job of predicting longevity.  (Read more:  What is the role of dairy cattle breed associations?) As the numbers show, today’s longed lived productive cow, may not look that pretty, but she sure milks that way.

Want to learn more about his? Andrew Hunt will be presenting at Canadian Dairy Expo on February 5th.


Comments (5)

If you haven’t worked in a trade show booth or attended a cattle show recently, you could very well be missing important genetic improvement discussions. Discussion about which traits breeders feel are at an acceptable level and which ones need to be improved. I suspect that few of you have worked a trade show booth but I can tell you, from front line experience, that bottom line focused breeders are not shy about saying that today’s dairy cattle are not functional enough, don’t get pregnant easily (may conceive but not retain)  and require too much worker time. Contrast that with the spectators at shows that talk about their ideal cow being tall, lean, tight uddered, deep ribbed and wide rumped.  Often front and center in all the discussions is which total merit index to use. Is it TPI, JPI, NM$, LPI, RZG, BW, TMI, NVI or another? Is any one total merit index capable of meeting the needs of all breeders?

Who is #1?

Every breeder or owner wants to have the #1 cow or bull. And back twenty to thirty years ago many bull owners bragged about having the #1. All-be-it they had the number one for Milk, Fat %, Fat Yield, Type or whatever. For the average breeder it was very  confusing. Which should they think was the #1 bull? In order to assist breeders, breed societies and genetic evaluation centers started publishing total merit indexes for bulls. Those indexes combined the production and type genetic indexes. It was reasoned that having a ranking system that combined all the traits was much superior to single trait marketing and selection.

Index Achievements & Short Falls

Recently CDN published the following genetic trends for Canadian Holsteins and Jerseys.

lpi & component improvement holstein canada

lpi & component improvement jersey canada

The average increase in LPI for both breeds is 65 LPI points per year. Undoubtedly this annual gain is more than would have been achieved without having the LPI to use for sorting animals. These gains are based on increases in both production and durability (conformation). But note that no gains have been made for health and fertility (H&F) in the past fifteen years.

Index Worship – Gone Too Far?

Having only one number to remember on an animal can be good but there can also be drawbacks to using only one number. These limitations include:

  • Everyone talks about the top ten TPI sires but in fact between #1 (Massey) and #20 (Goose) there are only 122 points. That is almost like getting 99% compare to 95% on a test. Not much difference. So drill down and know the facts. Indexes for these twenty bulls range from 42 to 93 lbs for fat yield and from 0.98 to 3.42 for Udder Composite.
  • Mating a high TPI bull to a high TPI cow without regard to where the bull and cow are strong or weak can lead to disaster.
  • Buying only on the TPI, even though the pedigree person announces that “this heifer is #1”, does not guarantee that you are buying the best animal for the traits important to you.

In fact we could very well have reached the point where we are limiting the advancement we will make in our herds because we do not look at all the genetic indexes for an animal. Instead of using TPI to sort out the top animals and then studying the strengths and limitations of an animal, we only consider the TPI. If you wonder about that The Bullvine suggests that you study the top TPI heifers looking at both their TPI and fertility (DPR) indexes. You will find many top heifers that have a negative DPR index. Is not reproduction the #1 reason cows are culled?

Which Index for You?

The key word in this title is YOU. What business are you in – the business of breeding and marketing of breeding stock or the business of milk production? After you make that important first decision, you are in a position to decide on which total merit index you should use.

It is important to think in terms of what you want your herd to be genetically in the future when selecting a total merit index to use. Traits beyond production and type are becoming more important to breeders. The following ICAR published table shows the relative trait emphasis for seven  leading total merit indexes and the average for all total merit indexes from seventeen countries.

Relative Trait Emphasis in Total Merit Indexes*

RANKNAME# OF DAUGHTERSPTATUdder CompF&L CompBody CompDairy CompStature
1BRAEDALE GOLDWYN553.032.592.561.932.033.1
2REGANCREST ELTON DURHAM-ET212.472.312.131.71.982.13
4REGANCREST DUNDEE-ET182.062.180.751.291.551.18
5GEN-MARK STMATIC SANCHEZ143.072.172.443.342.833.91
6WILCOXVIEW JASPER-ET112.891.940.732.562.523.22
7MAPLE-DOWNS-I G W ATWOOD-ET84.163.413.463.442.974.31
9PICSTON SHOTTLE-ET62.661.971.792.422.32.71
9ROYLANE JORDAN-ET62.071.940.321.532.061.93

* Reported by J Chesnais & Associates at 2012 ICAR Meeting (Ireland)

As you develop your breeding and business plans for the future, the following points may be useful to consider:

  • If you do not sell animals for breeding purposes, having type at a high weighting in your total index may not be your best business decision. NM$ may be a better index for you.
  • In ten years will you be a breeder or a milk producer? Choose either the breeder index (i.e. TPI or LPI) or the milk producer index (i.e. NM$).
  • If you do not show cattle or sell cattle to showmen, then PL (Productive Life) or HL (Herd Life) rather than PTAT or CONF should be an important part of your total merit index.
  • Including and giving significant weighting to traits such as fertility, longevity, calving ability, milking speed and mastitis resistance in the total merit indexes will be the way of the future for breeders focused on milk production.

The Bullvine Bottom Line

Total merit indexes are designed to rank animals according a set formula. After sorting out the top bulls on a total merit basis, breeders should use corrective mating to match the bulls with the cows in their herd. Not using genetic indexes denies you the opportunity to make significant advancements both genetically and from a profit perspective. Are total merit indexes helping or hurting breeders? It depends on knowing your genetic needs and using the index that focuses attention on your most important traits. No total merit index will best serve all breeders. Use the index that suits your plans (Read more:Fact vs. Fantasy: A Realistic Approach to Sire Selection, What’s the plan? and Genomics at Work – August 2013)

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.






Are you anxious about where dairy genetics are heading? How are you affected by the impact of genomics? Do you have concerns about health and fertility? What about the over-riding pressure to be profitable in a dairy genetics marketplace that sometimes resembles a global roller coaster of competing proof runs and bull lists?

Last week, I attended the Open Industry Session presented by CDN on behalf of the Genetic Evaluation Board.  I went into the meeting feeling interested and invulnerable because, after all, what you don’t know can’t hurt you. Right? But I soon learned I was wrong and not just because I was “a pair of genes short of a geneticist”.

DAIRY INDUSTRY TODAY: In the Running OR Run of the Mill?

On the plus side the Open Industry Session provides an opportunity for the manager and staff of CDN to demonstrate how they are fulfilling their mandate to fine tune genetic evaluations. It’s exciting to catch the enthusiasm for making genetic progress.  As pointed out throughout the day, a key measure of that progress is whether the science, the research and the results can be translated into on-farm applications for management, breeding and profitability.

Take A Genetic Bite Out of Mastitis

Mastitis is at the top of the list of 8 diseases that have an economic impact on dairy herds. Identifying genetic markers could have a significant effect on dairy profitability.  As with any index the quality of the data is the game changer here. Since 2007 40% of Canadian breeders have mastitis recorded. Prior to 2007 there is “ZERO” data. The good news behind those stats is that it is possible to build an index using correlated data from SCS and Type indexes.  In fact it was reported that Reliability gains were significant from using a multivariate model combined with historical data. The new genetic evaluation for Mastitis Resistance incorporates three predictors – Somatic Cell Score, Udder Depth and Fore Udder Attachment – as well as recorded mastitis, Body Condition Score and several other measurements associated with somatic cell count.  It reduces complexity by having one index that puts all the data together. This approach results in an evaluation that explains as much as 72% of the genetic variation in Mastitis Resistance and increases the accuracy of genetic evaluations provided by CDN.

disease frequencies

GENOMICS: The Fast and the Curious

Simplified estimation of DGVs allows CDN to move forward to more frequent releases of genomic evaluations for genotyped heifers and young bulls. Couldn’t help but sense the attention when BVD said, “We could release and update on a weekly basis.” The logistics appear to be fairly simple. “DNA genotyping labs would need to move to “continuous” genotyping for dairy animals.” VanDoormaal feels that at least moving information turnover from monthly to weekly (roughly from the current 6 weeks to 2 weeks) expands the opportunity for better decision making.

Bulls, Bias and Barriers

Genetic evaluations depend on data.  Huge volumes of data.  And not only is that data collected in 30 different countries but also with different methods, weighting and formulae. This means that bias is present and must be accounted for.  Canada has made extra effort to ensure that young bulls are not over-inflated relative to PT (progeny tested) bulls. Interbull GMACE can only recognize our GPA’s if we participate.  Italy, UK Canada and USA all plan to participate.

One of the most interesting opportunities for those at the industry session is seeing graphs demonstrating challenges, opportunities and actual genetic progress.

balancing genetic gain and diversity

impact of inbreeding on lpi and components

recessives trends - holstein

recessives trends - rw and polled

Take-home insights included:

  • 150 LPI points of genetic improvement represents $23.5 million dollars.
  • Graph representing within herd re-ranking of heifers with genomics. (There have been both high profile and large commercial herds regularly genotyping all heifers every year!)
  • With the right indexes and the right data it is ultimately possible to quantify the dollar value of right decisions vs. wrong decisions on heifers to keep as replacements.
  • Especially as regards inbreeding, dairy breeders are not paying enough attention to inbreeding. Therefore including it in the formula is a step forward. There isn’t significant loss in genetic progress but there is going to be population gain in having outcrossing taking place.
  • Adjusting Mendelian Sampling, by using only cow indexes based on male ancestors, can detect biased cow evaluations and thus determine the ones that are outliers (i.e. deviate excessively from Pedigree Index).

Each one of these breakthroughs represents tools that can be applied to improved profitability for the industry.

Canadian LPI:  The Less Stretched Index

Trying to boil down 1000s of hours of computerized “fine tuning” and “tweaking” into an easily understood Open Industry Session is a challenge for both presenters and audience.  With all the progress represented by the “new and improved” indexes the prime focus of the industry is to find the solution to bias in bull proofs.  “When we encourage industry participation, we hope dairy breeders care enough and are confident enough to stand up and try to make things change.”

Twenty years of a dynamic LPI has shown to be a great process.  That trajectory increased substantially with genomics. Now CDN is examining the best options for update to the LPI formula.  Two good questions were raised:

  1. “Are we going to lead with LPI or are we going to follow?”
  2. “Is there going to be breeder buy in to revised trait emphasis in the LPI?”

“Barking up the wrong fee!”  and “Who is responsible for this Hot Mess?”

Everyone attending the Open Industry Session requires dairy profitability for their daily survival whether that happens in a barn, an office, research lab, or at an editor’s desk. That is probably why ears perked up when the $7500 per bull fee for genetic evaluation results was raised … again!  It is a contentious issue for those A.I. organizations and some breeders who feel that they freely provide the information which becomes available to 30 countries. Therefore it should be available back to them.  Some feel the cost is too high. Others are concerned that too much or not enough information is disclosed. This oft-recurring and touchy issue makes its way to every open meeting where it is consistently deflected with the answer, “Fees are a policy decision not a genetics issue!”  Well then if this is an “open” session. Who sets the policy?  Who sets the fees? Who collects the money?  What is it used for?  If three out of four of these questions have the same answer, then let’s get to the table and make the decision and then live with it!


The meeting started seeing dollar signs again, after another perceptive question was raised, “If LPI is Lifetime Profit Index where does the Profitability come in?”  It was agreed that the aim is the profitable cow and we could do a lot better job of expressing the profitability value in dollars which is a language everyone understands.  That led to an “Aha!” moment!  It doesn’t matter how clear and accurate our calculations are, if they don’t translate well into the commerce side of the marketplace.  The key word here is “translate”. For those working in the global marketplace, language is another hurdle to overcome.   A few examples of how hard it currently is and how easily it could be done and it seems that multi-language translations of GEB / CDN publications is in the future.

The Bullvine Bottom Line

The Open Industry Session literally opens the doors to the future. We know what we want.  We know that time is passing.  We have the information and the means.  The final key is that dairy breeders, scientists and board members must have the will to move forward. Together? Are we dedicated to progress or just the perception of progress? The challenge is to figure out the answers and thereby shorten the distance between the future and the present.  Otherwise… A lot sooner than we think… we could end up on the outside looking in:  “Just a few great bulls short of a proof run!”

The Dairy Breeders No BS Guide to Genomics


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Want to learn what it is and what it means to your breeding program?

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I’ve been known to be random.  Quite random in fact.  Anyone who reads the Bullvine will find that sometimes there will be articles that seem to come out of nowhere.  This is because my mind seems wander all over the place sometimes and then all of sudden I get an idea and a thought for a new article or topic of discussion comes out of the blue.  The other day I was looking through my Facebook news stream and saw a picture of a turkey wrapped in bacon, which I shared of course because, in my unbiased opinion, there is nothing better than turkey and bacon together.  Nevertheless this is not a naturally occurring combination.  And, while delicious, it is definitely selectively controlled. This spurred the thought about the need to be random in sire sampling and how our young sire programs have gone from being random to totally controlled.

The Evolution of Genetic Evaluations

Prior to the introduction of Genomics, a young sire who was selectively sampled, say regionally, would have never been touched as breeders would have limited confidence in this sire’s ability to transmit when used in other herd environments.  That is because in order to get an accurate genetic evaluation of a young sire you needed to have young bulls sampled in many different herd environments where their daughters’ performance could be compared with contemporaries under a range of different circumstances.  This is the very foundation that our “Animal Model” is built on.

Over the years the way we look at sires has changed drastically.  First we looked at how their daughters’ average performance compared to other sires, with no regard for herd mate performance.  A method I see some old school breeders still using today.  In the 1970’s came the Modified Contemporary Comparison (MCC), which started to incorporate the performance of herd mates into evaluating sires.  This system was further improved to incorporate more information from relatives and resulted in the introduction of the full (cow and bull) Animal Model in 1989.

rate of genetic gain 60-86

It is interesting to see that if you look at the rate of genetic gain prior to 1974 (prior to the introduction of the MCC), you see that the rate has greatly increased since.


The five key factors that are considered in the animal model are:

  1. The cow’s management group
  2. The cow’s genetic merit
  3. The cow’s permanent environment
  4. The common environment of paternal-half sisters
  5. Other unexplained random environment

Where the problem lies is with that fifth factor” other unexplained random environment.”  Typically, that is meant to refer to the differences that still exist among cows’ records that haven’t been explained by other factors in the model.  In the past this was temporary as it does not affect a cow’s transmitting ability, as in the case of decline in milk yield due to mastitis flare-up.  The problem is this still assumed that everything thing was being done on a random basis with no herd and no selective sampling.

The Genomic Era – Not Random

The simplest way for the Animal Model to account for all things that cannot be explained is as a random event.  When spread over a large enough sample size, those random events will average out and we will be left with the true genetic merit of those animals we are evaluating.  That all worked just fine, prior to the introduction of genomics, when young sires where randomly sampled over many different herd environments, and a wide variety of dams with different degrees of genetic merit.  But with the introduction of genomics, no longer are young sires being sampled on just average cows.  They are now being selectively used on some of the highest genetic merit cattle in the world.  This is totally kicking that random principle out the window.

Young sires are no longer randomly sampled.  In today’s genomic age, a lot of the systems and controls are gone.  Yes, many of the sires are still offered to all breeders (well at least they say they are), but these high-ranking young sires are sold at a much higher price, and marketed much heavier.  In addition often the first release semen is only used on contract matings on extremely high index, carefully selected mates.  This results in anything but random sampling and in reality is almost the perfect method for receiving an inflated proof.  It isn’t just because of the actual mates they are being used on but also because of the care the resulting calves will receive.

Sure you can say that the Animal Model is supposed to account for this.  See bullet number 2 in factors considered by the animal model.  But is it doing so accurately?  Of even more concern is the bias resulting from the preferential treatment that offspring of the highest genomics sires receive (Read more:  Preferential Treatment – The Bull Proof Killer).  It’s only natural for these animals to receive this preferential treatment. The problem is that the Animal Model does not account for it.

This is not a new problem.  It’s just being amplified.  In the past this happened very frequently.  Just look at second country proofs of some elite daughter proven sires, Shottle, Planet, Man-O-Man, preferential treatment and selective use had these sire skyrocket to the top of the lists, only to settle back down once more random sampling occurred.  This is something we have already seen with Observer, His initial proof had him #1 in the US for TPI then once more daughters were added he settled to a respectable #8 among 99% reliable sires (Read more: Genomics at Work – August 2013).

One way this was dealt with in the past was to increase the minimum level of reliability for foreign bulls to receive domestic proofs.  In general this strategy was sufficient in the pre-genomic era, but even the centers that produce the genetic evaluations, such as CDN, are no longer finding this works in the current animal model.

The Bullvine Bottom Line

At the Bullvine we would love to say we know the solution.  The challenge is we don’t. Furthermore, I am not sure even those responsible for solving this problem have a clear grip on how to handle this.  Sure we could up the requirement for sires to receive their first proof, but is that really going to solve the problem?  What I do know is that time is of the essence. Within the next 12 months many of the sires that heavily promoted and selectively used post the introduction of genomics will be receiving progeny proofs in 2014.  If we don’t find a solution to this problem soon, we are all going to look as manufactured as bacon wrapped turkeys.

The Dairy Breeders No BS Guide to Genomics


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Want to learn what it is and what it means to your breeding program?

Download this free guide.





Low Heritability – High Importance

Wednesday, July 10th, 2013

The Bullvine is often asked, by our readers, why we place so much, or any emphasis at all, on Health & Fertility traits in our sire recommendations ((Read more: Bullvine Performance Index and Mating Recommendations). We have decided to share with our readers some of our thoughts on breeding for traits that have low heritabilities which includes many traits in Health and Fertility.

Which Traits?

On an individual traits basis we are talking about traits like heel depth (heritability 8%), daughter fertility/daughter pregnancy rate (7%) and calving ability / calving ease (6%). On a composite trait basis this includes Feet & Legs (15%) and Herd Life / Productive Life (10%).

Heritability Hidden

Experienced breeders know that there are difference between cow families in how they transmit for these traits.  To date we have not been able to analyse the data and produce accurate genetic evaluations for these traits. It is all about how we collect the data or analyse it.  For instance when a classifier looks at heel depth he/she is to score it compared to the ideal. Yet we all know the significant effects that hoof trimming (or the lack thereof), bedding keepers and cows walking in slurry all the time can have on the scoring of heel depth by the classifier. Likewise effectiveness of routines, management, environment, nutrition and season have a significant influence pregnancy. The same can be said for calving ease. Many non-genetic factors interfere with identifying the true genetic differences between animals. Little wonder that with using our traditional data capture and genetic evaluation systems we ended up with low heritabilities.

Ignoring Was the Solution

In short the inaccuracy and lack of adjustment possible for the data we have used to evaluate these traits has meant that we have not accurately identified the best or the worst on a genetic basis. As a result the majority of breeders have ignored the genetic indexes for low heritability traits and have relied on managing around any problems their animals have had or their sire selections choices created.

So Much in Composites

With composite traits there are many individual traits combined into one overall number for FLC / Feet & Legs and PL / HL. The end result can be a high or low score for the overall but, unless we dig deeper and find out the ratings for the individual traits, we do not know the actual areas of genetic superiority or inferiority of animals. Classifiers combine many descriptive traits for feet and legs to come up with the overall score for Feet & Legs. Of course, for genetic evaluations for longevity we can not wait for a cow to complete her time in the herd. We therefore predict PL / HL by a calculation that is a combination of SCS, DPR/DF, Udder Depth and Milking Speed. These are all significant factors in how long a cow stays in a herd, but still are an estimate at best.

Genetic Evaluations

The data we have had available has not been complete enough, with enough related details, to calculate accurate genetic evaluations for these traits.  We therefore have called them low heritability traits. In fact it could well be that the extent of the data captured is not complete enough to produce accurate results.

Until about 1950 breeders used raw, unadjusted data to base their cow and bull selections on. Virtually zero progress was made in advancing the genetic merit of dairy cattle. Any advancement made was usually made at the herd level by owners that were more fortunate in the animals they owned. Evaluation techniques following that time have included dam-daughter comparisons, contemporary comparisons, BLUP (sire model) and then BLUP (animal model). These were each improvements on their predecessor yet even with the latter the accuracy of predicting a young bull or heifer’s true genetic merit for low heritability traits was only about 25-30% Reliable. The end result was that breeders paid little attention to the genetic indexes for these traits. They hoped that by breeding for the traits of high heritability, they would more often than not be lucky and make some improvement in traits like heel depth, fertility and calving ease. Over time A.I. organizations addressed the low accuracies for these traits by having at least one hundred daughters in sire type proofs and more than three hundred observations in conception, fertility and calving traits.

Progress Made

Over the past six decades, the genetic progress has gone from zero for all traits to rapid advancement for the most heritable traits (i.e. milk, fat & protein yields, stature, udder depth, teat placement, rump width, ..etc.). Over the past two decades calving ease has been a concern for breeders. With the move to hundreds of observation recorded and analysed some genetic progress appears to have been made. But not so with longevity, feet and female fertility.

Important traits

Breeders know and often state that they see these traits as being very important, in the future, to their herd’s profitability.  Labor and input expenses to treat problem animals, loss of production and animals too long in the dry pens can be robbing farms of ten to twenty-five percent of their profits. Yes, important but the means to improve genetically has not been available.

Along Comes Genomics

As our readers already know, The Bullvine strongly recommends the use of genomic indexes in making breeding decisions.  The primary reason for that is that the accuracies of the index predictions are almost double for all traits what they were with Parent Averages. For female fertility reliabilities have gone from 30% to 55% when genomic results were added in. That is huge.  It means that breeders no longer need to ignore or hope for the best with low heritability traits like they did in the past.

All A.I. sires are now genomically tested and therefore have 55 to 65% reliable indexes for longevity, fertility and calving ease when they are released for use. Breeders can now place much more trust in the genomic indexes for these traits than they could in the Parent Averages from the past. (Read more: ACCURATE GENETIC EVALUATIONS: Can We Hit the Bull’s-eye?)

Health & Fertility in Total Indexes

Health & Fertility make up 35% in NM$, 33% in the Bullvine’s BPI (Read more: Bullvine Performance Index), 29% in TPI™ and 15% in LPI of the emphasis in these total merit indexes.  The reason for that amount of emphasis is because of their importance to the profitability of operating a dairy farm.

What do Breeders Need to Do?

Breeders need to decide which total merit index best suits their needs.  Some will use only one index while others will use more than one index. No matter which index is used it is always best to corrective mate using the genetic, preferably genomic, index of both the bull and the cow.

For the female side this does require that the herd be milk recorded and type classified and that all females be genomically tested. The expense of recording is a very worthwhile investment to better decision making. Remember new information is continually coming available on genomic results for areas beyond genetic indexes. Parentage verification, heifer management and disease resistance are just the beginning.

The Bullvine Bottom Line

Great forward strides have been made with genomic testing and it is no longer a matter of yes or no in using genetic indexes for Health and Fertility traits. Doubling index accuracy to 55 to 65% is a quantum leap. The future is very bright for enhanced genetic improvement and herd profitability for breeders that use all the tools.


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Breeders like to have benchmark numbers that they can refer to when selecting bulls, buying embryos or selling animals. Numbers like 2000 TPI™ just a few years back were unattainable but now have been surpassed. Some breeders are saying that they cannot keep up with the fast pace while others are taking rapid breed advancement in their stride. The Bullvine decided to study and report on the genetic advancement that has been made over the past few years.

Continuous Turnover at the Top

Five to ten years ago TPI™ for the top USA proven sires remained the same in composition and value year after year.  Back then proven sires stayed current for three to five years. Well that has changed.  We have new norms on the rates of change and the length of time daughter proven bulls are used heavily. From April 2012 to April 2013 ten new bulls entered the top twenty TPI™ list and the average TPI™ of the top twenty increased by 44 points going from 2150 to 2194.  In Canada fourteen new sires were on the top twenty LPI list in 2013 compared to 2012 and the average LPI was 292 points higher. No longer can breeders pick a bull and expect him to remain a list topper for at least three years.

Expecting More of Young Sires

The rate of change is even more evident in the young unproven bulls. Table 1 contains the averages for the top twenty young sires by year of birth. The source for this information are the CDN files and reports as these were readily available for the young sires genomically tested and sampled or about to be sampled in North America.

Table 1: Average Young Sire Indexes

Birth yearLPIMilkFatFat %ProteinProtein%CONFMammaryFeet/LegsStrengthHerdLifeSCSDaus Fertility

Note * Not all young sires born in 2012 have yet been released for sampling
All indexes listed are on a 2013 base

From the top twenty young sires born in 2009 to those born in 2012 their LPI  increased by 80 points per year. The 2012 crop are significantly higher for their type indexes with higher values also for Herd Life and Daughter Fertility.

The top twenty young bulls born in 2012 and that will be sampled are all by high genomic young sires with fifteen of them from dams whose sires are proven bulls.  The genetics industry continues to change at the rate that bulls are used and then replaced by other newer sires that are superior.

Heifers Rise Higher Too

Our study and analysis on heifers could only go back to 2011 as by 2013 they are milking and their own performance forms part of their indexes. However Table 2 shows that the top heifers have higher fat and protein yields and percentages and high indexes for Herd Life and Daughter Fertility. These are important changes for breeders that sell or buy embryos or heifers. Many of the points that the Bullvine has been recommending are being seen in the top heifers: – hold on to milk yield but increase fat and protein yields and percentages and pay more attention to productive life and fertility.

Table 2: Average Heifer Indexes

Birth YearLPIMilkFatFat%ProteinProtein%ConfMammaryFeet/LegsStrengthHerdLifeSCSDaus Fertility

Note * Only includes heifers born January to April in 2013
All indexes listed are on a 2013 base

The Bullvine Bottom Line

Both breeders and marketers of dairy cattle genetics face the reality of faster rates of genetic advancement and animals remaining list toppers for shorter periods of time. The trends seen in heifers of holding the milk while increasing fat and protein and increased emphasis on longevity and fertility can be expected to continue.  Genomic evaluations have been a major contributor to these changes but so also has breeder acceptance of the need for long lived profitable dairy cows that are able to perform while requiring less labour. With each new index release run breeders can expect to see new list toppers. Use the best and move on from the rest.

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





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Understanding and correctly using genetic indexes is important to breeders who derive a significant portion of their profit from dairy cattle breeding decisions. Major changes in the expression of indexes do not occur frequently but when they do occur it can be a time of confusion and perhaps lack of trust. The Canadian total index, LPI, has been used for over twenty years by Canadian breeders, as well as by breeders from other countries who source genetic material from Canada. When changes occur in the LPI indexing system, as is the case just now in April 2013, it is important that the reasons for the changes and the results be understood and incorporated into breeders’ decision processes.

Why Change?

For some time now the LPI values, especially for Holsteins, have been increasing quickly for all animals but it has been most noticeable for animals that have genomic evaluations. Breeders questioned how these young animals with indexes that are about 65% reliable can be significantly superior to recently proven top end bulls and active cows with their own performance values. As most breeders refer to the absolute LPI number, significant differences between the leaders on the various listings left doubt in accuracy in breeders’ minds. For breeders who think is bottom line terms and do not follow the LPI numbers closely, comment were often heard about the fact that numbers are numbers but it is annual cow profit that pays the bills, expands the business and sends the kids to college. Point being that the LPI difference between animals over-stated the net dollar difference between animals. These questions, comments and concerns were heard loud and clear by the CDN’s Genetic Evaluation Board so it studied the matter and took action.

LPI Scaling

The extreme range (-3500 to +3500) in Canadian Holstein LPI values had many drawbacks. It assigned most older long-lived profitable cows a negative value thereby telling a story that was not true and limiting the saleability of their subsequent generation. It assigned values that indicated significant differences between animals when the actual dollar differences were not that large. And due to the scaling effect for animals at the very top of the breed it gave values far exceeding the actual differences.  This latter point was especially true for bulls and heifers with only parent averages and genomic evaluations.

While studying possible solutions, CDN noted that in other major dairy breeding countries the scale for their total merit index is much much smaller than Canada’s 7000 point range. CDN decided to adopt a publication methodology for the LPI similar to what the TPI™ has used for many years. That involves calculating a value and adding a ‘constant’ to it.

New LPIs

Effective April 09, 2013  the new LPI formula is ½ Previously calculated LPI  + Constant.


Note that the highest progeny proven sires do not change in value.


Note that the range in values of Holstein LPIs is now much more similar, although slightly more, than the range for  Holstein TPI™

Sire LPIs

It is important to note that this re-scaling of LPI does not re-rank animals. But it does bring the progeny proven sires and genomically evaluated young bulls much closer in their values.


It is important to remember that LPI is the Canadian system for ranking animals according the weights assigned to the numerous genetic indexes of important for lifetime profit. For Holsteins the weights at 51% Production, 34% Durability and 15% Health and fertility while for Jerseys those weightings are 57%, 33% and 10% respectively. Breeders wanting to place more or less emphasis on the various can calculate their own rankings using  the CDN calculator available at or going the Bulvine’s bull listings for alternative ranking systems (Read more: Bullvine Performance Index (BPI) – Top Sires December 2012).

Using Genetic Indexes

Indexes are a very constructive tool to genetically breed better animals for the future. As genetics is less than half of the reasons animal differ in profitability, much depends on breeders to not only produce the animals that will be profitable but also to feed and manage them.  Some suggested ground rules to follow when making sire or heifer selections are:

  • Use LPI, TPI™ or Net Merit are you primary list reduction tool for sires or herd replacements
  • Always check out the index values for the traits important to you (i.e. protein, fat, feet & legs, udders, SCS, fertility,..). Eliminate animals from the list that do not meet your requirements.
  • A quick way to eliminate animals is to use % RK (percentile rank).
  • Animals below 75% RK for any yield or conformation traits will likely leave progeny that reduce your profit.
  • Animals below 60% RK for health and fertility traits will not move your herd ahead for these traits of emerging importance.

The Bullvine Bottom Line

Even though the method of expressing genetic indexes may differ from trait to trait or country to country, it is always important to have a plan on what you want to improve genetically  in your herd and then to select the sires or replacement females that will produce the results. The re-scaling of the LPI values will come closer to the actual dollars amount animals return in their lifetime profit and will more accurately compare older and younger animals. By all means keep your genetics current and on target to your needs. It is best to throw out the semen from low indexing bulls. Buy high ranking genetics. It always pays big dividends.


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Three times in the past two weeks serious dedicated dairy cattle breeders have asked the Bullvine questions that we too have been wondering about.

QUESTION 1: Why do we accept breeders collecting DNA samples but not owner recorded milk weights?

QUESTION 2: Why can’t milk weights from robotic systems be considered for publication purposes?

QUESTION 3: Why don’t milk recording programs take all relevant details about a cow when the milk yield data is captured?

We decided to turn those queries into a think piece so that even more breeder input can be brought into the discussion.

The Reality Is

The current data included in national data bases is based on what was the norm a couple of decades back. As well it is based on the previously accepted fact that only human eyes could determine if a recording was accurate or unbiased.

Times have changed. Today robots milk cows without human oversight. Technology is coming out every year on ways to capture more details that can help in breeding, feeding and managing dairy animals.

It is true that individual owners own their animal’s data. They paid for its capture, but only through having all the data for dairy cows in one or inter-linked data systems will breeders be able to advance their animals as quickly as possible.  No one breeder is an island onto themselves so the approach must be to use and make available all the animal data.

The reality is that it is time to put energy and resources into addressing the needs and possibilities when it comes to the data captured, stored and reported.

Capturing Cow Data

In both robotic and large herds owners do not milk the cows. The computers or cow milkers have no bias towards any one cow. Also systems are being used in some tie stall barns where the RFID tag identifies the cow and the system electronically captures the yield. In these systems the data is captured for each and every milking.

QUESTION 4: Why is that data not available for others to see?

QUESTION 5: What can be more accurate than recording every milking?

Surely we are not prepared to argue that eight to ten single milking observations in a lactation by a third party person is more accurate than every milking captured by the milking system.

Canada found twenty years ago that owner recorded milk weights and collected milk samples were accurate enough for sire proving purposes. Data that is 95% accurate is much superior to no data at all.

In the foreseeable future there will be parlour systems that can instantaneously provide readings for butterfat %, protein %, SCS, milk temperature and hormone levels and we expect in time readings for fat composition, protein composition and a host of other readings. Wow won’t that be useful information to use to breed, feed and manage?

Question 6: Will this further information be moved off the farm into the national data system?

Just last week it was reported at the Progressive Dairy Operators Conference that RFID ear tags may have use for measuring temperature and ear movement to monitor heats in tie stall barns. That is interesting.

Data Starts Early

Calves are to be identified at birth with RFID tags.

Question 7: Why is it not possible to use technology that now exists to collect a piece of the ear tissue for DNA analysis?

That way every animal would have a DNA profile at birth. With the very interesting things we are learning on DNA profiles and heifer management, we have just scratched the surface of this crystal ball.

Calves are now being fed by computers from day three or four of age. There will potentially be a very useful data set there that can be of great benefit when determining genetic merit, feeding programs and management practices.

Let’s Dream the Possible Dream

But it does not end there! Many other details and data sets exist that are not part of the national data base but that can be useful for animal traceability, food safety (mastitis and other drug treatment), foot care, reproduction, production limiting diseases (i.e. Johnes), pedometers, rumen boluses (i.e. temperature),… and the list goes on.

Question 8: Are plans being made to link all dairy cattle data bases?

But Is It Official?

In the past, if a piece of information could not be authenticated then it could not be published.  In the future, every farm using genetics to advance their animals will, out of necessity, need to capture and use more data than they have ever had to in the past. Official and unofficial applied when breeders were or were not prepared to trust the method of data capture.

In today’s world there are many systems of marketing and commerce that are monitored as necessary but without a third party observing every event. Breeders are routinely putting on Facebook events about their cows, including their milk yields, an animal’s profit per day, flushing history and ability to come into heat when milking 120 pounds per day. The world of dairy cow information is changing and changing quickly.

QUESTION 9:  What does the current “official” actually mean in the bigger future scheme of things?

The Bullvine Bottom Line

THE ALMOST FINAL ANSWER: Future data standards will need to address that more information will be needed and that data must be universally available. Breeder input is needed now to guide the development of future standards for data captured, stored and reported.


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The udder may be a cow’s most prized physical asset, but her feet and legs literally provide the support for everything she does. How many situations with problem cows boil down to problems with their feet and legs?

In most herds foot care and hoof trimming are considered to be a very necessary event and, therefore, an expense that cannot be avoided. With this absolute in mind, we tend to march on breeding, feeding and managing cows without taking the time to consider ways to stop merely treating the symptoms we`re stuck with. Solving the problem before it becomes a health or management problem could completely avoid starting our animals off on the wrong foot. The Bullvine invites you to consider the genetics of feet and legs with us to stimulate a breeding solution for these issues.

The Heels of a Dilemma

In milk recorded herds, culling cows for feet and leg problems is #1 on the list of conformation culling reasons. In the past, udder breakdown was once the leader. However breeders have placed sufficient emphasis on improving udders that we are now to the stage where milk producers are saying they do not need to select bulls for udder traits except to avoid ones that are too deep.  It’s encouraging to know that with focus and time identified problems can be solved.

Although removal of horns may be the current hot button for people concerned about the welfare of animals, and therefore breeders are selecting for polled, there are numerous reports predicting that lame cows will be the next and much larger target.

Certainly, there are no dairypersons who are saying that feet and legs are good enough that genetic improvement for feet and legs is not needed.

Locomotion is Costing Us an Arm and a Leg

Reports show that for a cow with one temporary sore foot it reduces her annual profit by at least $100.  So what is the cost of a cow with foot construction that requires trimming 3-5 times per year, medication, less milk production, milk withdrawal, extended calving interval and premature culling? Feet and leg problems could be costing some herds $300 per cow per year.  On a one hundred cow herd that is $30,000 less profit. Significant by anyone’s standard.

A Vet Looks at the Genetics of Lameness

Gordon Atkins, DVM and a member of Holstein Canada’s Type Classification Advisory Committee, was a speaker at the recent annual meeting of the Wisconsin Holstein Association. He is not prepared to accept the fact that feet and leg heritabilities are as low as they currently appear to be.  Additionally, he shared some interesting facts about feet and legs:

  • Lameness is 88% a rear foot situation
  • That leaves only 12% for it being a front feet and leg problem
  • The outside rear claws bear the brunt of the lameness issue
  • The fact is that the rear outside claw grows faster because it is growing tissue in response to the greater pressure it endures while walking
  • Thin cows have a higher incidence of lameness
  • Thin cows mobilized fat from their bodies including the fat from the foot pad or digital cushion within the base of the heel structure. This results in less protection for the foot and heel.
  • The foot’s fatty pad can be replaced as the cow regains body condition but over time scar tissue will form when adequate fat is not present in the pads

Dr Atkins went on to highlight

  • His very telling statement followed, that being, “we need to evaluate feet and legs better”


Diagram – cross section of the foot

Diagram – Cross Section of a Bovine Foot

Let`s Go Toe to Toe with the Facts Only Please

Let’s summarize:

  • Dairy cattle have a genetic problem relative to feet and legs especially for animals not allowed to get off cement or to exercise
  • It is rear feet that are the major portion of the problem with respect to lameness

The Achilles Heel for Classifiers

The classification system scores numerous traits but there are factors in the area of feet and legs that are beyond their control.  Foot angle is not a good trait to measure because it is so variable due to foot trimming. Cattle owners have feet trimmed before classification so type classifiers do not see the animals in their natural state.  Classifiers do the best they can, given the circumstances. Add to this the fact that classifiers do not see every cow walking. Since the ability to walk is what is most important, classifiers again are at a distinct disadvantage.

Estimating heritability using classification data shows these percentages:

  • 30% for bone quality (moderate)
  • 24% for rear legs side view (moderate)
  • 13% for rear legs rear view (low)
  • 11% for foot angle (low)
  • 8% for heel depth (low)

Yes the report card is in – we need to improve the evaluation feet and legs especially for rear feet and rear legs rear view. Genetically we have bred for thin cows and thus less fat in the foot pad. The only place we collect feet and leg data for genetic purposes is in the type classification programs and there the classifier, as mentioned, is at a disadvantage. What’s left that breeds, classifiers, people doing the genetic evaluations and breeders can do?

Getting a Toehold on the Solution

A collective approach is needed:

  1. We must admit that we have a problem and that we need to find a solution to more accurately knowing the genetics of feet and legs.
  2. The problem is not limited to one country and it is more prevalent in cattle not allowed to walk on natural surfaces.
  3. Resources (people and money) must be allocated to investigation and research.

Some suggestions the Bullvine has heard on ideas to consider include:

  • observe or measure the females over their lifetime
  • evaluate the feet on calves at weaning
  • evaluate the feet on heifers at first breeding
  • measure the feet on first lactation females on their first milk recording test day (before they are trimmed)
  • compare sire’s daughter feet and legs on confined versus pastured daughters
  • compare the genomic profiles of cow families that are both desirable and undesirable for feet (and legs)

It is encouraging to see that there is one hoof trimmers’ guild that has public support for a study to collect pedigree information at the time of trimming, to complete a report of the condition of the feet before trimming and then to have the data analyzed. That could be a start.

In the Interim… Feet Forward

Research takes time and cows are bred every day, in the mean time, breeders must use the information currently available from sire indexes or proofs. It is strongly recommended that sires be highly ranked for Net Merit, TPI or LPI and higher than 1.5 FLC or +7 Feet & Legs. A recent addition to the information to consider on bulls is their Body Condition Scoring index. Bulls whose daughters do not get as thin during lactation should not drain all the fat from their foot pads.  (Some Bullvine recommended sires to use can be found at From Fantasy To Reality – Top Sires To Address Herd Culling Problems)

The Bullvine Bottom Line- “Stop “Digging in Our Heels”

What is needed is an international approach to studying dairy cattle feet, much like the approach being taken to studying feed efficiency.  Hopefully a way will be found to move feet research in dairy cattle to the DNA level. If the industry collectively has the will, there will be a way. All we need now is a champion to take the first step.


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The Bullvine is often asked, “How can using genomic sires be better, if the genomic sire’s reliabilities are not as high as those for proven sires?” So in typical Bullvine style we set out to answer that question.  The following is our answer…

Single Trait – Fat

Bullvine wanted to keep this comparison as simple as possible.  To do this we used one trait, in this case fat yield, knowing that breeders do not select for one trait only. The results apply to all traits.

Females in Your Barn

You have a virgin heifer and a seven year old cow that are both indexed at 100 kgs for fat yield.  Both have been genomically tested and the cow is milking in her fourth lactation.  The heifer’s index is 67% Rel.  and the cow is 82% Rel.

TABLE 1: Females

Born Fat Index % Rel Regressed Fat Index
Heifer 2012 Jan 10 100 67 67
Cow 2005 Jan 16 100 82 82



Three sires you might consider using for breeding these females could be:

TABLE 2: Sires

Born Fat Index (kgs) % Rel Regressed Fat Index
Oman March 08, 1998 82 99 81
Supersire Dec 28, 2010 116 67 78
Pride January 27, 2012 135 69 93


Index of Calves

What will be the fat indexes for the resulting calves? (Add parents together and divide by two)

TABLE 3: Regressed Fat Indexes for Calves (kgs)

Heifer 74 72.5 80
Cow 81.5 80 87.5

These values are the expected average fat indexes.  And, yes, there will be less variation amongst the progeny for Oman and the cow.  The most variability amongst the progeny can be expected for the heifer when mated to Supersire or Pride.

Therefore, the short answer for which bull to use, is Pride. Pride will maximize the calf’s fat yield index.

Rate of Genetic Gain

Determining genetic gain is a principle taught to all college genetic students.  The formula is:

Let’s simplify this:

Accuracy                              =             Reliability

Selection Intensity          =             Determined by where the animal ranks in the population (all these animals are in the top 1% of the population so their selection intensity is identical)

Genetic Variation             =             Standard Deviation of fat yield indexes (common for all the animals in the example)

Generation Interval        =             The average time between the birth of the parents and the birth of the calf.

Generation Interval is the place where the numbers for the heifer and the sires, Supersire and Pride, are much smaller (in years) than those for the cow and Oman.

TABLE 4: Generation Interval (years)

Heifer 8.5 2.5 2.0
Cow 11.5 5.5 5.0

Since the numbers for fat index in TABLE 3 are all similar, dividing them by a larger vs. a smaller generation interval greatly affects the outcome for genetic gain.

For the cow and Oman dividing 81.5 (Fat Index) by 11.5 (Generation Interval) gives a much smaller gain than for the heifer and Pride (80 divided by 2.0).  In fact it is much different 7.9 compared to 40.

That’s the reason turning generations more quickly, using genomics, gives the faster rates of annual genetic gain. (Read more: The Genomic Advancement Race – The Battle for Genetic Supremacy)

The Bullvine Bottomline

Genomics gives you more speed.  No question.  If you’re worried about speed being dangerous, spread the risk by using multiple (not one) high indexing genomic sires where you might have only used one or two proven sires in the past.



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No one likes paying upfront fees for anything.  After all, what’s the point of paying for something you haven’t received yet?  But there are some situations where paying upfront totally makes sense. Getting genetic information is one of those times.  You give up your money first and it translates into rewards later.

The Pieces are Put Together to Pull Together

Twenty years ago in Canada the dairy industry was faced with a challenge.  Government said it would fund research and development but not genetic evaluation services.  The goal was to shrink the cost and size of government.  The industry said these reports are valuable so we are going to have to get involved and that is what happened.

logo_cdn2_0[2]Canadian Dairy Network (CDN) was established in May 1995.  General Manager, Brian Van Doormaal, has been with CDN since its inception and summarizes the general details. “CDN is governed by a Board of Directors that primarily consists of breeders who are elected as representatives from four categories of member organizations, namely Breed Associations, DHI Agencies, A.I. organizations and Dairy Farmers of Canada.

The Canadian Dairy Network provides five major services:

  • Genetic Evaluation Services
  • Research and Development Projects
  • Industry Standards
  • Maintains the National Dairy Data Base
  • Operates the Data Exchange amongst the industry partners

It`s Fully Integrated and Always Moving

In the simplest terms, all the relevant information is shared by those who contribute.  Examples are:  Breed pedigrees go to CDN; CDN shares them with everyone who is a partner; DHI records go to CDN and are shared with partners.  These and more types of information are available to all users at all times via the Internet.  Everything can be found at the CDN website AT NO CHARGE for lookups.

The Dollar Division

Van Doormaal updates the funding process behind CDN. “All activities of CDN are financed by the industry organizations that are its members and for this reason the CDN Board of Directors has established an equitable service fee structure.” He further breaks out the pay structure. “80% is paid by AI and 20% by breed associations and milk recording provide their information at no charge to CDN.”

FEES: Fearsome Hurdle or Forward Thinking?

When there is a 79% cost increase (effective April 2013), there are going to be questions. Namely, “How did CDN determine the cost of $7500 to prove a bull in Canada?”  Previously the fee was $4200. The same fee has been set on a per bull basis for privately owned genotyped bulls, starting April 2013.  CDN does not have any other fees so this is an all-inclusive rate that gives the bull owners access to various services associated with genetic and genomic evaluations.”

Van Doormaal further clarifies. “With the arrival of genomic evaluations in 2009, operational costs have risen due to increased staffing needs and computer power while the number of young bulls with semen released in Canada each year has almost halved.”  Obviously, the plan is three-fold:  provide more research; more development and, at the same time, cover costs into the future.

Everybody Pays!

Van Doormaal stresses that, “In one way or another, all people and organizations will be paying fees to receive genetic and genomic evaluation services from CDN for bulls. While the mechanism for paying differs for breeders compared to A.I. organizations that are members of CDN, the level of payment is equivalent.  On the female side, no fees are applied on an animal basis since the breed associations contribute to funding CDN activities on behalf of their members.”

Brian Van Doormaal, CDN Speaking at the 2012 China-Canada Dairy Conference

Brian Van Doormaal, CDN
Speaking at the 2012 China-Canada Dairy Conference

What’s Up in Other Countries?

Van Doormaal knows the international scene and explains, “While there are other countries like Canada for which the genetic evaluation services are financed completely by industry stakeholders, as opposed to government, each country inevitably ends up with its own funding formula and mechanism.” He speaks of the American situation.  “In the US, the mechanism proposed for financing its genetic and genomic evaluation services includes some level of fee applied to every male and female for which a genomic evaluation is to be calculated.”

Proving Your Own Bull

When asked about advice for breeders looking to prove their own sires, Van Doormaal urges. “Genotyping young bull calves shortly after birth makes as much sense for breeders as the genotyping of their newborn heifers.  Once the genomic evaluations are available to the breeder, better decisions can be made about the bull’s future.  Owners (AI or breeders) of bulls with outstanding results can then pay the CDN fee to make results official and have the young bull ranked among others available in Canada.”

LPI Formula Changing

Van Doormaal reports “The LPI for Holsteins in Canada currently has a range in values of approximately -3000 to +3000, which is three times bigger than the TPI in the United States and over 50 times bigger than national indexes used in most other countries.

The CDN Board of Directors decided, after consulting all stakeholders, that the LPI scale should be halved.  To achieve this objective while maintaining the current level of LPI values for the highest progeny proven bulls, it was decided to add a “constant” value to the LPI formula in a manner similar to what the United States has done for years with its TPI formula. Conversion from current LPI values to the proposed new scale is simply done by dividing the current LPI in half and then adding the constant of 1700.”

LPI Formula Give and Take

Another adjustment Van Doormaal expects to happen to the LPI formula relates to the specific traits included and the relative emphasis placed on each.  Analysis of various options and discussion will proceed through 2013 with a likely implementation of an updated formula in April 2014. Based on feedback received from a cross-section of breeders, there seems to be a general interest to increase the overall emphasis on longevity, fertility and disease resistance in the formula. Of course, once the emphasis is increased on some traits, there also has to be other traits losing emphasis.

Future CDN Genetic Evaluation Evolution

In December 2012, CDN introduced Body Condition Score as a newly evaluated trait for all breeds, which can be used as an indicator for fertility, disease resistance and longevity.  The release in December 2013 will include the first official genetic evaluations for Mastitis Resistance in all breeds which should be followed by Resistance to Metabolic Disorders in 2014.  Other traits on the planning horizon within the next five years include desirable fatty acids and other components of milk, hoof health and feed efficiency.

Changing Gears for Genomics

Van Doormaal provides updates resulting from the introduction of Genomics. “Prior to 2009, CDN had six different genetic evaluation systems, which were run monthly to evaluate over 60 traits including production, type, longevity, female fertility, calving performance and milking speed/temperament. With the arrival of genomics, a new system was developed and implemented, which estimates Direct Genomic Values (DGVs) for all traits and combines them with traditional evaluations to produce the published genomic evaluations.  This new system is also run monthly and also required the establishment of a national database to process and store all genotypes, which now totals over 310,000 across all breeds. Operationally, these new services that are highly valued by the industry organizations and breeders, have required additional geneticists and new web site development as well as investments in advanced computer equipment and processing power.”

CDN: Providing Global Genetics and Genomics

Looking to the future, Van Doormaal gives an overview. “The era of genomics is still in its embryonic stages.  It is difficult to predict the extent to which it will continue to impact the dairy cattle industry over the next 10 or 20 years.  One thing for certain is that the world of genetics will continue to shrink at an increasing rate since it is so easy to collect DNA from any animal in the world and assess its genomic evaluation on numerous country scales.”

CDN:  Fine-Tuning

CDN will dedicate much time and effort in the coming years to fine-tuning existing traditional genetic evaluation systems and methods for estimating genomic evaluations. Van Doormaal is realistic about the possibilities. “The shift towards a higher market share held by genomic young sires compared to progeny proven sires will likely experience some pendulum swings, eventually reaching stabilized proportions as breeders and industry gain experience in the coming year.”

After 25 years working and educating in the Canadian proving system, Van Doormaal is proud of the achievements. “We are fortunate in Canada to have many geneticists and research scientists who realize that the ‘practice’ of genetic selection and mating is not the same as the ‘science’.  Both sides need to continue to respect and listen to the knowledge and experience of the other. The most progress is made by incorporating the ‘science’ of genetic improvement into a solid, practical breeding program.”


Recognizing the potential of responding to changes in the industry, in technology and from science, CDN is focused on the future on behalf of breeders.




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Every country loves to tell you that they have the best Genetics in the world and that their cattle are superior to any others.  At a recent International Committee for Animal Breeding (ICAR) Session in Cork Ireland, a group of leading geneticists got together to discuss lots of highly scientific and many mind boggling things.  Tables upon tables of stats and graphs that look more like maps of the solar system and would make most people’s heads spin.  However, from that session there were some really interesting presentations about genetic improvement around the world that just needed to be “translated” into dairy speak.  The following is the Bullvine’s attempt to de-nerd the nerdy.

Look Who`s Talking

Canadian Dairy Network Researchers, along with an associate, presented a paper entitled “Genetic improvement: a major component of increased dairy farm profitability’.  To be totally honest it was the ‘profitability’ word that first drew our attention but on reading the paper, studying the power point presentation and listening to the video of the presentation on the Internet ( we garnered many interesting facts about the genetic merit of bulls and genetic trends by year for many traits in seventeen countries for the time period 1997 to 2006.  Sixteen of the seventeen countries studied were sampling more than 200 dairy bulls per year and in the USA both the TPI™ and Net Merit were included in the analysis since both are widely used total merit indexes.

Genetic Progress –Which Countries are winning the genetic race?

Are breeders in these 17 countries making genetic progress?  Definitely yes!  It is difficult to compare across countries given the multitude of ways of expressing sire proofs for traits across countries.  Therefore, the researchers converted the expression to standard deviation units (SD unit) and summarized the results in the accompanying graph comparing the time periods 1997-2001 to 2002-2006.

Yearly genetic progress by country and trait

Yearly genetic progress by country and trait (bulls born 2002‐’06)

It is interesting to see that while many of the major genetic markets in the world are advancing at similar rates, the Nordic countries are giving the United States a run for their money and the Canada was the sixth fastest advancing country, almost 18% behind the genetic advancement rate of the US and the Nordic Countries.

Canada`s NOT First

So I am sure many of my fellow Canadians are saying that we are ahead in the race, others may be gaining on us, but we still have the best cattle there are.  Well folks I hate to burst your bubble but as the following chart shows, for bulls born in 2005-2006, it’s actually the United States that are out ahead followed by France and Italy.  Canada comes in sixth, behind the Nordic regions and the Netherlands.

Average EBV of bulls born 2005‐'06 'for the 17 country average index

Average EBV of bulls born 2005‐’06 ‘for the 17 country average index

Genetic Progress by Trait – The Leaders and the ‘Also Rans’.

  • Protein Yield: Increasing rates of genetic gain have been achieved by all countries except for Ireland and New Zealand where progress has been flat lined due to the major selection emphasis being on fertility and other management traits.  The leaders for the increased genetic progress in protein yield are France, Nordic Countries and the Netherlands.
  • Overall Udder: The rate of genetic progress for udder is also building at an increase rate with the leaders being Italy, Canada and the USA.  Selection for udder improvement was not part of the breeding strategy in New Zealand and Ireland and no genetic progress was made for udders in those countries.
  • Longevity: Very significant progress was made for longevity in all countries with the leaders being Ireland, Italy, New Zealand and the USA with France following behind the rest of the pack.
  • Somatic Cell Score:  No genetic gain was made in any country from 1997-2001 for SCS.  However that turned around after 2001 and all countries made progress with the leaders for genetic progress being the USA, the Nordic Countries and Canada.
  • Calving to First Service: Ireland and New Zealand have made progress since 1999 and are significantly out in front of all other countries.  For the other countries there was negative progress until about 2003.  Since then all countries have started to give attention to this trait and the tide has turned to where slight progress was being made by 2006.  After Ireland and New Zealand, The Nordic Countries are leading the other countries in increasing their rate of genetic progress for this fertility trait.

So what happened to production?

There is Reduced Emphasis on Production. By way of example the researchers provided a graph (below) showing how The Netherlands and Ireland have gone from 100% emphasis on production traits in their total merit index in 1995 to approximately 30-35% in 2012.  While the USA and Canada have been more moderate in their reduced emphasis on production traits, from 70% to 45-50% in their 2012 total merit indexes.  There is more to breeding than all out selection for production but it is still an important component in the total scheme of things.


Relative emphasis in national selection indices

Relative emphasis in national selection indices

What Traits are Driving Progress?

When you take a look at the average genetic progress by trait across countries (graph below) you  see that the rate of genetic advancement in each area reflects the relative weighting change in each country`s  major index.  With the rate of genetic gain on longevity, health and fertility greatly improving and that for the production trait (protein) actually showing a slightly slower rate of genetic gain.  It is interesting to note that in the period of 1997-2001 the primary emphasis on protein improvement actually had a negative impact on the rate of improvement for fertility.


Average genetic progress by trait across countries

Average genetic progress by trait across countries

Different Strokes for Different Folks

As the chart below indicates, the relative weights each country put on each trait in their national indexes has a huge impact on the rate of genetic gain for those traits.  We understand that not every country dairy’s under the same circumstances.  Hence why for Japan places 72% of the emphasis on protein, fat and milk while the Netherlands places 26% of the emphasis on protein and fat yield.  Ireland and then the Nordic countries place the most emphasis on Health, Fertility and other management traits.  South Africa then USA (TPI™), Spain, The Netherland and Canada place the most emphasis on overall type.  Italy places the most emphasis on udders.  In addition, the USA (Net Merit) places the most emphasis on longevity.

Relative weighting of selection indices worldwide

Relative weighting of selection indices worldwide

The 2012 average weights placed on the various components in the 18 indexes are:

  • Production 48%
  • Type 17%
  • Longevity 11%
  • Fertility 11%
  • Udder Health  8%
  • Other  5%

Increased emphasis on functional traits in most countries has resulted in more genetic progress for these traits.  These advances were achieved without a reduction in the rate of progress for key production and conformation traits and without the use of genomic selection, since that new tool was not yet available. As genomic genetic evaluations were not occurring from 1997 to 2006, it will be interesting to see the trends for the five and ten years following 2006 when extensive use of gnomically evaluated bulls has occurred.

The Bullvine Bottom-line

Neither the art nor the science of dairy cattle breeding is dead.  In fact it can likely be said that rates of genetic improvement are about to accelerate.  Are we ready to keep up?


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Accuracy of bull proofs has been one of the biggest challenges for dairy cattle improvement for many years.  It has been well known that top index cows have always received some level of “preferential treatment” and as a result their indexes have been inflated.  Usually this didn’t affect their sire’s proof since they were usually already proven sires and when weighted with many other daughters this had little to no effect on the sires proofs.  Enter genomics and large portions of young sire daughters receiving preferential treatment and this could have huge effects on the proofs of these genomic index bulls.  There is no question that the current systems around the world cannot account for this preferential treatment and as a result many genomic sires’ first proofs will be inflated.

In the past when young sires were sampled they were used across many different herd environments and regions.  I remember when regionally proven sire (California, etc) or breeder proven sires were released. Many breeders where hesitant to use them because they were not confident that these sires proofs would hold up.  Young sire programs in the past offered semen at low cost or pretty much free (when you factor in incentives) to many different breeders in order to ensure that the sire got enough daughters and that they would be able to achieve a reliable proof.

Does random sampling still exist?

Young sires are no longer randomly sampled.  In today’s genomic age, a lot of the systems and controls are gone.  Yes, many of the sires are still offered to all breeders, but these high-ranking young sires are sold at a much higher price, and marketed much heavier.  In addition often the first release semen is only used on contract matings on extremely high index, carefully selected mates.  This results in anything but random sampling and in reality is almost the perfect method for receiving an inflated proof.  It isn’t just because of the actual mates they are being used on but also because of the care the resulting calves will receive.

Why do daughters receive preferential treatment?

Think about it, if you have paid upward of $750 for a dose of semen (Read more – $750 Dollar Semen! Are you crazy?) to be used on your most valuable animals, wouldn’t you make sure you protected your investment by giving them the best care possible?  It is well known that top index cattle around the world have received over inflated indexes as a result of preferential treatment.  The problem is ‘how do we account for the biases?

Does the current system account for preferential treatment?

Genetic evaluation systems assume that all animals in the herd are treated equally.  Yet while there is nothing wrong with a breeder wanting to ensure their return on their investment in these top genetic animals, it certainly causes many problems when accounting for it in the genetic evaluations of these animals. (Read more – The Hot House Effect on Sire Sampling).

Most “animal-model” genetic evaluations in the world account for the genetic merit of a sire’s mates.  However, when the US first added females to their genomic reference set they actually got lower reliabilities as a result of inaccuracies in female’s proofs due to preferential treatment.  That is why some countries actually leave female genomic data out of their reference sets, as a large portion of the females are these high index animals that, in many cases, have received preferential treatment.  In the US they actually implemented a scaling-effect adjustment to bring those top females down.  The US has also implemented a new single-step model that includes genomic and traditional data together designed to account for this in bull proofs.  Other countries are also looking for potential solutions.  This includes potentially withholding early data from evaluations as well as other options.  The challenge is that no one has found a real solution to the actual problem, and steps so far just mask the issue with scale downs and other band-aids.

How to identify preferential treatment?

I recently attended a GEB session put on by CDN (Canadian Dairy Network) where they gave a presentation on accounting for herd bias.  Brian Van Doormaal presented a few different ways he theorized would identify bulls’ daughters who might have received this preferential treatment.  One indicator he presented of possible preferential treatment was if a high percentage of a bull’s early offering were the result of ET.  Another indicator he looked at was the percentage of daughters that have been genotyped.  However, neither delivered conclusive results.  Another suggestion that was presented was increasing the number of daughters a sire needs  in order to receive an official proof.  The challenge with that is that A.I. companies and most high profile breeders are wanting sires to get a proof as quickly as possible and increasing the requirements will cause delay.  In addition, analysis of semen price so far does not show it to be a great predictor either.  Currently there are simply no answers.

In Brian’s presentation he equated this problem to the challenges we have seen with second-country proofs.  In Canada bulls like Shottle, Planet and more recently Man-O-Man (Read more – Man-O-Man will he turn platinum? and Is Man-O-Man really going to be a sire of sons?) that come through with initial Canadian proofs over 3500 LPI, which everyone knows to be unrealistic, in time saw their proofs drop 300+ points with the addition of more daughters.  Van Doormaal also comments that you could expect bulls like Snowman, and genomic sires to do the same.

The Bullvine Bottom Line

Currently there are no definitive answers only growing concerns.  This preferential treatment problem is going to get greater attention, as more high profile genomic sires,  priced high and highly marketed will start to receive proofs in 2013. The industry must be proactive about this issue. If not we are going to see breeder confidence in proofs decrease, instead of increase, because of genomics. That would be a killer!

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





Everything You Need To Know About TPI and LPI

Thursday, August 23rd, 2012

How much do we really understand the TPITM and LPI system? Do we really know what they mean and what their limitations are? Earlier this week CDN General Manager Brian VanDoormaal posted an informative an interesting article, ‘Canadian Pride of the Canadian Kind!’, on the CDN website comparing and contrasting TPI™ and LPI, the national indexes for the USA and Canada. This got us here at the Bullvine thinking, maybe it’s time to revisit just what these indexes mean, why we have them and what their limitations are.

A New Tool was Needed

These indexes started in Canada and the USA for a number of reasons.  In 1984 Holstein Canada had adopted its breeding strategy whereby equal emphasis was to be placed on type and production yet almost two animal generations later breeders often continued to practice single trait selection – for show type, for conformation, for fat percent, for other traits. Marketers were all claiming to the #1 bull for this that or the other thing. In short the strategy was not being followed and the benefits of moving the population forward were not being achieved.

Setting the Standard for Continuous Improvement

TPI and LPI were introduced at relatively the same time and their primary achievement was to set a common base for breeders to rank their animals. Both indexes were first used over twenty years ago and have been continuously improved. Since starting as a way of combining type and production TPI™ and LPI have been enhanced by attaching economics to the traits.  This relates back to the breeders bottom line. The indexes have been adjusted to norms and standard deviations. For instance, milk yield is a big number and conformation is a single number, but their relative importance may be more closely related than the numbers alone would indicate.  Having said that, it was a good move to remove milk yield in favour of fat plus protein.  We don’t need to be shipping water or forcing cows to producing more and more low component milk.  Next conformation traits used in the indexes was limited over time to those of most economic importance on the farm. More recently the indexes have added health and fertility traits.

These are all worthwhile enhancements. Yes these indexes have been dynamic over the past two decades but have not been changed so frequently that they have lost the trust and support of the users

How to Use the Indexes

Today we make multiple uses of  TPI™ and LPI:

  • to select parents especially bulls to be used,
  • to market both males and females,
  • to follow the breed’s breeding strategy specifically indentifying the animals that best combine the traits and weightings in the strategy
  • used as culling tools within a herd or population primarily for proven bulls. Cows are most often culled for one or two economically limiting factors they have.

And the most important use of TPI™ and LPI

  • To rank animals based on the breeding strategy.

Moving the Population Forward!

It is the breeder’s and breeding companies that use the rankings to move their herd of the population forward. Since the traits in these indexes frequently have zero or negative correlations with each other, the indexes are a way to rank animals and come up with what is often referred to as ‘balanced breeding’. Animals with show type and production well below average or high production and low type, do little to improve herds or breeds.

Indexes Go Beyond the Numbers

Wouldn’t it be great, if you could just combine this LPI or TPI number with this trait you’re trying to improve and , “Voila!” you have the progeny that will improve your breeding program?  In 2012, when we are using, TPI™ and LPI we must be mindful that they include composite and predictive traits that are independent or negatively associated with each other. This means that the number in the index cannot be seen in the milk pail, in the eye of the breeder or in the bottom line of the farm. For instance a cow or bull with 3000 LPI – where do you see that number? It’s the combination of factors that is important. Simply stated, the indexes are a way of comparing the merits of animals.  The significance is in the comparison not in the number itself.

So what are the Results?

Since the adoption of both TPI™ and LPI, breeders and breeding companies have been able to significantly improve their herd and move the breeds forward according to the breeding strategies. The results can be seen in the udders in the barns and the volumes of fat and protein in the bulk tanks to name just three components of these indexes. Less obvious are the results for less heritable traits like feet and legs, SCS and the more recently added traits for female reproduction and longevity. Measuring the results of breeding is not easy or free of complication. Variables on each farm such as nutrition, housing, labour, management and environment can all impact the breeding results.

Annually CDN publishes the changes in many traits for the Canadian dairy cattle populations. These changes are estimates of the genetic gains made in the previous year. In 2012 the published changes for Holsteins include LPI +160, fat +3.4 kgs, protein +2.4 kgs. Conformation+1.05, Mammary System +0.93, Feet & Legs +0.81, Herd Life +0.50, SCS -0.03 and Daughter Fertility -0.27.  As you can see progress was not made for all traits. This happens because animals in the population are the result of breeder decisions and not the result of having a national breeding strategy. We do not have access to the results for the USA however we expect that they would mirror those in Canada.

Are There Limitations?

Yes there are two limitations.  First, as mentioned, TPI™ and LPI points cannot be seen by the human eye, measured in the bulk tank or on a farm’s financial statement. Secondly TPI™ and LPI function as if breeders are mating animals evenly rated for all components in the index. In actual fact, every bull and every cow has both strengths and limitations. Neither the absolute average nor the perfect animal in the population has ever been achieved. Each time a breeding decision is made, breeders must consider the attributes and limitations of both the male and the female in the population along with the objective of that particular mating and not just take the TPIs™ or LPIs of the parents, add them together and divide by two to get the resulting progeny!

The Bullvine Bottom Line

Even though TPI™ and LPI have limitations, they are beneficial tools to use in improving the genetics of North America’s dairy cows. There is no doubt that these indexes will be refined and improved in the future. The dairy cow of the future will be even better. Genetics does make a difference!


As more and more early high genomic young sires are getting their daughter proofs in next week, I am sure we are going to hear that the sky is falling.  And yes, while there is much certainty that the bulls may drop, that in no way indicates that genomics does not work.

As early proofs have indicated, the large majority of genomic sires will drop.  But that should not have everyone running for the hills.  Instead, what you should do is look at 2 key metrics:  1) How they compare to the proven sires that where available at the same time as the breeding  2) The percentage that are returned to service.

Why genomic bulls may drop

While critics would say that any drop is not acceptable, that just shows that they do not understand how the system works.  There are other reasons that bulls may drop that most breeders may not consider;   here are a few reasons:

  • Hot House Effect
    While we all would like to believe that the system is faultless, that is just not the case.  It’s important to remember that proofs are first and foremost based on herd variation and genetic gain over their parents.  So if a genomic sire is used on a dam who maybe lost a teat, or was sick as a calf and did not develop to her full genetic potential, this will have a huge advantage for the genomic sire.  Same is true if breeders are looking to work that system.  By that, I mean they are going to have other genomic cattle in the herd that do not receive the same level of attention as the families that they are working to have succeeded. (read more here:  Has Genomics Knocked Out The Hot House Effect)
  • Higher Quality Dams
    In the past, young sires were used on G and the odd time a GP dam, but never on your high scoring 2yr olds.  But with genomics, we see sires being used on VG 2 yr olds.  Unless the progeny can score higher than the dam (not account for herd variance), it will be next to impossible for that bull to receive a positive type proof, let alone one that will allow them to be a breed leader.   However, the potential for these sires to have the exact opposite effect is very possible, for instance, they were used on a VG-87 2yr old and her resulting progeny ending up a GP-80 2yr old.  The sire will actually receive a much lower type score as a result.  In reality, it is better to compare and note the similarities between a genomic sires daughter proof to a 2nd crop proof of the past.
  • System Improvements
    As mentioned in the hot house bullet above, the system is not perfect.   These early proofs are based on the best educated guess that the geneticist could do given the data provided.  As more data is available it will be possible to refine the system.  The most useful data they will get will be these early genomic sires with daughter proofs.  This will allow them to see how effects such as being used on higher quality dams will have and how they can adjust the system to account for this.

Does it matter?

The critics will say that the AI companies could care less if the bulls drop.  They have sold so much semen on these young sires at such high rates that they have already made their profit.  And yes, this is partly true.  There is no question that a high genomic young sire will probably become a significant profit as compared to the past when they were a $50,000 investment.   And then there is still the issue of credibility.  It does not take long or many sires killing pedigrees before the clients of these AI companies will start losing business. The other part of the equation is that often these same AI companies have used these sires as sires of sons in their own programs, resulting in a significant risk for their programs and future profits as well.

The Bullvine Bottom Line

What breeders need to remember is, yes, genomic sires may drop.  But instead of running around like Chicken Little announcing the sky is falling, what they need to do is compare those same sires to the proven sires that were at the top of list at the time when they made the breeding decision.  From a systems perspective, it is better to look at what percentage of these genomic young sires are return to service.  This will indicate if the system is working or not.

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





From old school dairy breeders telling you, “They are all worthless!” to geneticists telling you “They are the greatest thing since sliced bread!” it can be challenging to figure out whether tools like TPI® and LPI have significant merits in your breeding or marketing program

What Are They?

To get a better understanding of what each of these indexes represent start with the fact that  TPI® (Total Performance Index) and LPI (Lifetime Profit Index) are multi-trait indexes.  They both combine production, type, and health and fertility traits to rank sires on their ability to transmit an economic balance of these traits. TPI® is calculated by Holstein USA and LPI is calculated by The Canadian Dairy Network.

The big thing to remember about both of these indexes is that they are more or less a predictor of a bull’s ability to transmit based on established weightings.  For TPI® that weighting is as follows

TPI Formula

Source: Holstein USA, click on image for more details

Whereas LPI has the following weighting, 51% production, 29% conformation and 20% health traits. As you will notice, LPI actually puts a greater weighting on conformation and health than does the TPI®.

They’re Tools You Fool

The big thing to remember is both of these indexes were created to help identify superior sires that combined high production, sound conformation, and desirable health and fertility traits.  It does not mean that these sires are the only sires you should be using.  Or that if you only use these sires you will have the best herd in the world.

What it does mean is that you can use these tools to help short list what sires you are wanting to use, assuming that you are breeding for high production, conformation, and fertility.  If you are like some old school breeders who feel that high lactation production is not worth the tradeoff then fine, LPI and TPI® are not for you.  In reality, each breeding program would be best to develop their own index based on the needs and goals of their breeding program.  Maybe you would want more emphasis on health or type.  It all depends on your goals and then you work from there.

It’s All About the Marketing

Were these indexes created just for marketing?  No.  Were they created for ways to compare and sell sires?  Yes.  What’s the difference?  Well when both these indexes were created they had all the right intentions.  They were created for a way to compare sires on their overall genetic merits.  Which lead to major sale and marketing opportunities for those organizations and breeders who had the top sires.

I can remember that, before these multi-trait indexes were introduced,  everyone claimed to have the #1 sire or cow.  While that is still happening, for the most part TPI® and LPI provide the opportunity for breeders to gain a clear understanding of who is the top sire for producing high production, sound conformation, and healthy cattle.

The Bullvine Bottom Line

With so many different traits that are evaluated, trying to identify which sires have the overall best genetics can be very challenging.  While the TPI® and LPI formulas may not be the exact weighting that works for your breeding program, they are designed to represent that average breeder (if there is such a thing).  They are designed to give opportunity to compare sires on relative merits and see which sires rise to the top.  The big thing to remember is that they are to be used as tools! If you lose focus on that, these tools can have you looking like a fool!


Before the recent Kueffner Kows at Cowtown Sale Horace Backus, commented that he had never seen anything like it in all his years!  “The quality of every animal and the homebred breeding was just so good.  Just before the sale started, I took a moment to walk through one of the lines of cows while it was quiet and everyone was already gathered in the tent.  I stood looking at a line of maybe 40 animals, and thought I was standing at Madison seeing that many great cows all together.”  These comments reminded me of the ones he made before the 1998 Hanover Hill Dispersal where Horace said, “In the history of the Holstein Breed, there have only been four or five herds that have created a distinct blood herd.  Today we are selling a distinct bloodline herd.”  This got me think will there ever be another distinct bloodline herd?

Over the years, the marketplace has changed greatly.  The improvements in technology have been incredible.  It is now easier than ever to market, compare and transport your genetics to anywhere in the world.  To get a better understanding how each of these will play into the potential of having another distinct bloodline, we decided to take a closer look at each one.

Marketing to the World

In the era of Hanover Hill era buyers did come in person from around the world.  The world has changed greatly with the Internet.  I often wonder what a great marketer like Peter Heffering would have done in today’s time.  The ability to market to a much larger audience through the internet and Facebook is expanding the marketplace.  You are no longer just selling to the person next door or in the same country or the few who are able to travel to buy.  You are often selling to people half way around the world.  And more importantly than where they are, is how quickly and easily you can reach them.  You no longer have to run magazine ads in each country’s major breed magazine.  Today you simply post a quick smartphone picture, or better yet video, on your Facebook page and share it with the world.

Cross Country Comparisons

One of the things that contributed greatly to each country or region having its own distinct bloodlines was that the ability to compare performance data on in each country presented challenges.  In previous generations, it was hard enough getting everyone to talk in the same units (ex. Lbs. vs. kgs.) let alone the fact that they had different methods of evaluating things.  Then came Interbull and MACE proofs. That started to open up the marketplace, but for some the confidence in the MACE system was not there and for the most part most countries still had regionalized breeding and evaluating systems.  Then came genomics that has given breeders around the world the confidence no matter where the bull was proven to use him on their cattle.  We now see that there is no longer a negative stigma in North America on foreign proven bulls.  Moreover, many of the great international cow families are gaining significant respect in the North American marketplace, especially as sons of these cattle have proven themselves well on the North American genetic base.

Transportation of Genetics

All the great marketing and evaluation systems in the world mean nothing if you cannot get the genetics to the consumers.  Artificial insemination had a drastic impact on the ability of breeders to develop distinct bloodlines.  Instead of just running your own breeding program where you sell the odd breeding bull, artificial insemination meant that when you sold that bull to an AI center, he would now be able to reach the world market.  With AI companies also becoming less regional or country focused and more world focused, that meant you could sell a bull in Chicoutimi Quebec and his semen could be used in Kamifurano Japan.  Breeders no longer had to develop their own bloodlines and could draw on the best bloodlines from around the world.  Furthermore, as embryo transfer technology advanced you could also import and export embryos and further accelerate your breeding programs.

The Bullvine Bottom Line

Today breeding herds like De-Su limit the amount of genetics they sell and AI organizations like Select Sires are entering the female animal ownership side in order to develop a distinct product in the marketplace.  Nevertheless, I truly feel that with the overall changes in the global marketplace we have a much more level playing field through evaluation systems and technology and, therefore, it is highly unlikely that we will see the achievement of a distinct bloodline at the level reached by Hanover Hill.


Nobody wants to make decisions based on the wrong information.  Good breeders know that accuracy is the key to making successful breeding decisions. Wouldn`t it be wonderful to have perfect data at our fingertips? There`s nothing wrong with dreaming the impossible dream but, realistically, in the business of cattle breeding, you can’t wait for that golden sunrise when perfection is a sure thing and 100% repeatable.

THE PAST:  Almost-Perfect

Whenever we look back at animal-breeding history, a rosy glow settles over our perception of the past.  For more than fifty years, we have constantly improved our North American genetic evaluation methods and models, proudly proclaiming them to be, if not perfect, at least the very best. Many of us felt we were destined to be at the top in cattle breeding forever.  Then, the very success we reveled in spread our success and our genetics to everyone else. Accuracy was harder to ensure. Genetic evaluation methods and models are based on accurate recording of pedigree and performance data and all international input data is not created equal from country to country. Nevertheless we trusted the Animal Model (1989), the Test Day Model (Canada 1999) and Interbull (the international proof system). And it was still good.

AND THEN CAME GENOMICS:  New Dart!  New Target!

Hardly a decade into the 21st Century and Genomics comes along and changes our perception of the future.  Here is a revolutionary new tool or dart, if you will, to take genetic aim with.  Now there can be more focused selection much earlier in the bull or heifer’s life. Since that first official genomic evaluation in August 2009 accuracy has increased. Great! But now even the genetic target has changed.  It is bigger. Now we don’t only target selection of proven bulls and performance recorded cows, but selection of young bulls and heifers, shortly after their birth.  The full potential of what we can aim for has yet to be imagined.


In the interest of accurate information, it is important to look at everything that may be a negative influence on achieving this goal. In a May 2012 article entitled, “The Ongoing Challenge of Accurate Genomic Evaluations” Brian VanDoormal (CDN) points out those things that make precision targeting harder to achieve:

  • Non-random usage
  • MACE evaluations
  • Parent Average less accurate when the parents are foreign
  • Estimating unbiased proofs for foreign sires
  • High priced foreign proven sire semen used on higher quality females in higher quality herds.
  • Differential treatment adds to bias of non-random usage
  • Non-random usage of elite progeny proven sires
  • Non-random usage of high ranking genomic young bulls

VanDoormaal goes on to report that, “ CDN is actively researching methods to reduce or eliminate such biases and to better incorporate MACE evaluations of foreign sires and bull dams into Canadian genomic estimations and officially published proofs.” He emphasizes, “One immediate area of importance being researched is the development of methods to reduce bias in evaluations for foreign sires and bull dams.”

GENETIC EVALUATION ACCURACY: A Hard Target with Collateral Benefits

Each step that increases accuracy increases the trust that breeders can place in the information.  In fine tuning genetic evaluations we benefit from increased accuracy in predicting other traits that previously we didn`t have data on: calf health; fertility; resistance to disease; specific components of milk; hoof health.

Not only has the arrival of genomics changed how genetic evaluations are calculated but it has also significantly changed male and female selection strategies by A.I. companies and breeders as well as semen usage trends by producers. Even breeders who do not use AI will benefit from genomics because they will have available to them bulls that test genomically high but that were not selected for AI.  Previously there was a wider range of bulls sampled at great expense.  With genomics, the entire gene pool of sires is being much more accurately identified for their genetic merit.


For more than 100 years cattle breeders have moved the industry ahead by selecting for the traits they felt were most important. There was a progressive emphasis as the focus changed or was expanded:  amount of milk in a single day; total milk in a liftetime; butterfat; protein; and conformation. New models and young sire programs were developed. All of these had an impact but the potential for genomics impact is far greater.  With genomics, large numbers of young bulls can be tested and eliminated with an enormous reduction in time and cost to the breeder and the industry. This adds to the burden of responsibility for genetic evaluations to be accurate and account for non-random selection and/or under-evaluated progeny proofs.


Will Genetic Evaluations ever achieve 100% accuracy?  Only time will tell. The challenge we face now is to keep the system steadily improving for the impact having accurate information can have not only for cattle breeding today but for generations to come.

For more information check out our Genetic Evaluation Resource Center.


For some time now the Council on Dairy Cattle Breeding (CDCB) has been working to establish a “Cooperative Agreement” with the USDA Agricultural Research Service (ARS) pertaining to the transfer of the USDA-­‐ARS dairy genetic evaluation service to the CDCB.  This has culminated in the recent release of a draft Cooperative Agreement for public comment.  The problem is that the draft lacks some of the core values that makes America great, specifically the ability for everyone to operate on a level playing field (access to information) and to be led by brave leadership driving toward a better future.

With these changes come many questions.  Some key issues follow.

Will everyone have access to the information?

Reading the agreement may require having a law degree to fully understand it.  This may be by intention, but it really doesn’t make for light reading.  Some of the language in the proposed agreement is very confusing. It talks about how the CDCB will have ownership and control of the information.  One of the reasons that the USA has been able to become the mega world power that it is was because it was founded on the belief that everyone is created equal and has equal opportunity to achieve success.  Looking at how the use of genomic information was handled in the past does not bode well for how everyone will get free access to the information.  Many smaller organizations are concerned that this will lead to a monopoly for a few A.I. studs.

The proposed wording is in stark contrast to allowing free access to the information for all those involved.  This actually causes a double edged sword.  On one side, the powers that be are limiting the small guy from competing at the same level.  However, there is also the interest about keeping much larger players, such as say Pfizer from entering.  In Canada, Pfizer is already offering genomic testing and what’s to stop them from using their many resources to use that information in new ways (read Are You Ready for Genetically Modified Cattle).

How do we maintain our integrity with breeders worldwide?

Similar to the views expressed by Greg Anderson of Seagull Bay Dairy, many breeders are concerned about the perceived integrity that comes from going away from a government organization (USDA) to a private entity.  Vice President of Holstein USA Glen Brown and Director Bill Wright also express these concerns,  Both men are also  dairy breeders and call for the need to develop  strong business plan, in the following video


While I do understand this concern, there are many examples worldwide, such as the Canadian Dairy Network (CDN), which has been able to maintain integrity and do it   without the political hurdles that come with government involvement.

One of the lessons learned from the CDN model is that you need equal representation from all parties involved, not just those who put up the most money.  CDN is majority funded by Industry and specifically A.I., but its board has equal representation from breed associations, breeders, and industry.  This is necessary in order to maintain the integrity of the organization and also to provide effective direction for the future.  One thing is for sure, it will take bold leadership through these times.  This makes me remember when Murray Hunt (Dad for disclosure sake) backed by the Canadian Genetic Evaluation Board, was facing a similar challenge in Canada. At the time he made some bold moves, hiring of Paola Rossi, and Gerald Jansen, Canadians working in Italy to do Canadian genetic evaluations, long before there was the full business plan, but rather had the agreement in principle.  Yes, this was putting the cart before the horse, but it also lead to the formation of the Canadian Dairy Network (CDN).

Who pays the bills?

As Holstein USA Director and dairy breeder Leroy Eggink, points out in the video above, it has been a great scenario for US breeders having taxpayers foot the bill.  But, that gravy train is over.  In Canada when that ship sailed, it left industry footing the bill.  Since A.I. represents the most direct profitable gain from genetic evaluations, that means they are left holding the bag. Ultimately, this cost is passed on to the breeders.  And while the response comes that we pay for all the systems that track and record this information, there is still the cost to convert that raw data into actionable information (bull proofs).

The one area the CDCB needs to remember is that all costs should be expensed equally and should not play favorites with the larger A.I. centers, as happened with Genomic information.  In an interview with Ron Flatness, Flatness International, he repeatedly expressed the concerns around price for the smaller competitors and protecting against un-needed additional fees.  (Following comments are that of the writer and not Ron) Instead of higher membership fees that will limit the involvement of smaller organizations or independent breeders, all costs need to be handled equally.  One standard price per sire sampled vs. a much larger membership fees, would be fair to everyone.

The Bullvine Bottom Line

Be careful what you ask for.  While many breeders want 100% free access to information, it isn’t always a good thing.  While there are many questions that still need to be answered, regarding a business plan, ownership of information and how to be as transparent as possible, I ask the question, “Is this a move to keep, not smaller players, but much larger players out of the marketplace?”

Here are some more great resources:

Dairy producers will have 29 days to comment on the Cooperative Agreement (May 7 to June 4).

If you have questions please contact any of the CDCB officers.

Contact information for USDA representatives:



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