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Genomic Testing – Are You Missing Out?

Thursday, August 21st, 2014

When The Bullvine mentions genomic testing to production oriented breeders, we frequently get the reaction “Oh, that’s just for herds that sell high priced animals. I focus on running a profitable milking operation. I don’t need to spend money on testing my animals.” Well, in fact, that is not an accurate assessment of the benefits available from using this tool at the present time. If you are among those not using genomics, Stop Procrastinating! It is a tool that everyone breeding their herd to improve it genetically should not be without.

Only Very Moderate Uptake – So Far

Currently, there is an 8% uptake of genomic testing of all Holstein heifer calves. The total is less in other breeds. We have barely scratched the surface.  Half a century ago, official milk recording was at the same low level. Today it is recognized as a much-needed toll both on-farm and in the national herd. Obviously the question that breeders need answers to is ‘How will I benefit from genomic testing all my heifer calves?

Known Benefits

Much has been written about benefits and opportunities available to breeders who are submitting samples for DNA testing. Those range from selecting the best mates for your females, … to parentage verification, … to how to manage your heifer herd, … to deciding which heifers to breed and which ones to cull or implant, … to polled or not polled, …to finding the genetic outlier of an individual mating, …to an aid in marketing heifers in sales.

Just recently Holstein USA and Zetas launched an exciting service called Enlight. Breeders that submit their samples to Zoetis can through Holstein USA’s website summarize and analyze their heifers for their genetic qualities. This is the first, and no doubt other breeds will establish similar services in the future. Breeding to get the genetics that work best for you and then managing them in the best way possible is definitely important.

At the industry level, genomic testing has also proven beneficial. Alta Genetics, a few years ago, working with large herds in the USA, parentage verified all young sire daughters. It was a significant step forward in accuracy of sire proofs so they could guarantee their product to their customers. Companies like Zoetis and Neogen initiated genomic testing services so they could help producers and also as complementary to their other products. A.I companies have been able to restrict their young sires sampled to only top genomically evaluated young sires, thereby saving millions for themselves by not sampling the bottom enders and millions for breeders that did not have to raise, calve in and milk the lower genetic merit daughters of the bottom end bulls. All of these benefits are leading to cost savings in the hundreds of millions of dollars.

However six years into using genomics we are only starting to reap the rewards.

Genomics Will Make the Future Brighter

Breeders often mention that they want sires to use and females in their herd that are superior to what is available today for traits that are difficult or impossible to measure. Here are some thoughts and facts that may help breeders to decide to use genomic testing so they can have animals that are even more profitable than their herd is today. It does however require that genomic testing becomes routine (Read more: Why 84% of Dairy Breeders Will Soon Be Using Genomic Sires!).


Investigation, at the farm level, is being done in beef heifers on growth rates, diets tailored to genotype, immunity to common diseases and age at first estrus. The results of those studies will be able to be applied to dairy heifers since little similar research is being conducted for dairy heifers. Already breeders can test for the genetically inferior heifers, so they do not need to be raised. Up to $500 per heifer in rearing cost could be saved by having the retained heifers calving by 22 months of age.  Remember that it is age at first estrus that is important, for which we have very limited farm data. First breeding depends on a breeding actually occurring.  With heifers genotyped and selected for first estrus significant savings will be possible.

Feed Efficiency:

Two major research projects, one in USA and The Netherlands and one in Australia and New Zealand, will identify the cows that are genetically more efficient at converting their feed to milk. Within a couple of years, we can expect to see reports relating genomic information to feed efficiency.  This type of research is costly and not currently practical at the farm level, but using research herds this investigation is well underway. Reducing feed costs by 5-10% through genetic selection would result in many millions in savings. That is likely to be crucial to the dairy cattle breeding industry as dairy competes to feed a hungry world. (Read more: Feed Efficiency: The Money Saver and 15 Strength Sires That Will Still Fit In Your Stalls)


CDCB already makes available the inbreeding level of genomically tested animals based on their genomic results. No doubt further research results will provide numbers associated with inbreeding. Think about it. In the past the inbreeding level for two full sisters, based on pedigree, has been considered the same. However, by using their genomic profiles the level of inbreeding can be much more accurately known for each sister. A recent report from CDN, for the time period 2010 to 2013, shows that inbreeding rates are increasing not decreasing. Even though breeders are aware that inbreeding is a negative to future profit, they continue using fewer sire lines. More in-depth study of presence or absence of genes that negatively affect the viability of our cattle take time. Why do we always expect someone else to take responsibility for the level and rates of inbreeding? (Read more: 6 Steps to Understanding & Managing Inbreeding in Your Herd and Stop Talking About Inbreeding…)

Disease Resistance:

The list is long on diseases that breeders want their animals to be resistant to. Many research projects are underway to relate the genotype to particular types of mastitis, respiratory diseases, wasting diseases and even production limiting diseases like milk fever. CDN and Canadian milk recording agencies have been capturing field data for a number of years now on eight production limiting diseases. In time, the relationships between genetic lines and these diseases will be better-known. So that selection can be carried out to avoid problem bloodlines. When more animals are genomically tested, and bloodlines prone to diseases are identified great steps forward will be able to be made. It takes considerably more than 8% of the population genomically tested to move breeding for disease resistance to reality. (Read more:  Genomics – Opportunity is Knocking)


Failure to get animals to show good heats, to produce good oocytes and conceive when bred is the leading frustration on most dairy farms. The role that genetics plays in that frustration is now receiving attention by many researchers and organizations. In the past, the capturing of useful data to do genetic analysis relative to reproduction has been a significant problem. The relating of genomic results to reproduction holds out considerable hope. Early embryonic death, haplotypes that negatively impact reproduction, genetic difference between animals for cystic ovaries and many more are all areas of concern for breeders. Once again both genomic and on-farm data are needed to move forward. (Read more: 10 things dairies with great reproduction do right and Are Your Genetics Wasting Feed and Labor?)


I hear breeders say “Genomic indexes are just like production indexes.” However, that is not so. There are genomic indexes for production traits, conformation traits and management traits. Genomics is a dynamic science. It is best if breeders know not only the genomic values for the animals currently in their herds but also their ancestors. To build the genomic history for a herd necessitates that testing start as soon as possible. Genomics is a tool every breeder will benefit from using no matter what their selection goals are. (Read more: Better Decision Making by Using Technology and FACT VS. FANTASY: A Realistic Approach to Sire Selection)

In Another World

Outside the world of dairy cattle but totally related to DNA analysis, there is a study just under way in the United Kingdom, where 100,000 people with cancer or rare diseases are being genotyped to better understand people’s ability to avoid or resist cancer and disease. One of the terms used in the news release was that before there was DNA profiling this work would not have been possible. Relating that back to dairy cattle, if we do not have the DNA information for animals we will be limited in our ability to eliminate deleterious genes from our cattle.

Will Genomic Testing Pay?

The question for breeders appears to have been one of cost – benefit. “What will I get for the fifty dollar cost of doing a low-density test?”  The fact is that, to date, milk producers have not taken the opportunity for more rapid genetic advancement by testing all their heifers. However, the tide is about to change. With new information coming out almost weekly on how the genetic (aka genomic) make-up of an animal relates to profitability, breeders without genomic information on their herd will not be in a position to know which sires to use or how to manage or feed their animals. Genomic testing needs to be viewed as an investment rather than a cost. Invest $50 shortly after birth to save hundreds over the cow’s lifetime.

The Bullvine Bottom Line

Every journey requires that a first step be taken. The first step is that breeders submit samples for DNA analysis. Every breeder will benefit by knowing the genomics of their herd. No doubt the cost of testing will come down as more breeders participate.  Future success in dairying will require genomic testing, just as current success depends on capturing and using performance information. Are you prepared for using genomic information to assist in creating your future success in dairying?

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?

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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


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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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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Zoetis is a global animal health company with 60 years of experience.  Zoetis, formerly Pfizer Animal Health, was a business unit within Pfizer Inc.  On February 1, 2013, Zoetis became a stand-alone animal health company.  Zoetis is a publicly traded company on the NYSE.

When DNA profiling in herds, the program at Zoetis is to get dairy producers to focus on genotyping the entire heifer group.  This allows breeders to make selection and management decisions, before investing the full cost of raising each heifer.  Depending on where breeders are located, the cost of raising a heifer ranges from $2000 to $3500 (Read more: Should you be raising your own heifers?) By testing animals at a young age, breeders can decide if they want to sell the heifer, breed her to a beef sire, use her as an embryo recipient or consider flushing her.  It’s about making accurate choices and, ultimately, profit.

Which Benefit Category Works for YOU?

  • Do you have an excess of heifers?
    DNA profiling means you can manage your heifer inventory more precisely and invest your rearing budget in the heifers that you need to keep.  Keeping control of the heifer inventory also has an indirect health benefit. Reduced numbers prevents heifer facilities from being overcrowded. A less stressful environment reduces calfhood and heifer diseases. Remember that heifer rearing is the third largest on-farm cost after labor and feed.
  • Do you use sexed semen?
    This higher priced tool can be best applied to the top 50% of heifers based on their genetic merit. Doing so is a significant step toward elevating the genetic potential of the next generation of heifers in your herd.
  • Is your herd unregistered? 
    You have the most to benefit from genomic testing because you will be going from zero genetic information to more genetic information than you could ever get from simply registering your animals. Now you can make better selection and mating decisions.
  • Is profitability your first priority?
    The top priority profitability traits for most herds are selection for milk components, with the remaining emphasis on traits that contribute to longer herd life (SCS, DF, HL, F/L and mammary).  LPI is a great index to use as a first sort in selecting the most profitable animals.

Analysis.  Assessment.  Action.

Zoetis has developed the “CLARIFIDE” program. Veterinarians are trained in understanding the basics of genomics and how this information can be integrated as part of the herd’s management program.  There are over 100 veterinarians across Canada that have been given the designation of “CLARIFIDE Accredited Veterinarian”.  Many of them underwent a multi-day training program taught by representatives from Zoetis, CDN, Holstein Canada and Semex. Today, if a local vet has not been trained through the CLARIFIDE program, but they have a client that is interested in submitting through CLARIFIDE, Zoetis will conduct training with these vets either in person or on-line.” Dr. Melodie Chan, Zoetis Business Lead and Manager Veterinary Services, concludes. “With access to this information, breeders are able to allocate their resources more effectively.  As genomic research progresses, we may even be able to consider health protocols to match each animals’ potential to respond – such as response to vaccination.”

Clarifying Genetic Potential

The goal of every dairy breeder is to identify and act upon the genetic potential of their dairy animals. “Through the CLARIFIDE program, Zoetis has worked closely with its Alliance partners.” says Dr. Chan, who outlines the benefits and potential. “By working closely with CDN, Holstein Canada and Semex, the CLARIFIDE genomic consulting program offered through Zoetis provides a truly Canadian perspective. Furthermore, this Alliance has also fostered research initiatives and collaborative funding towards projects that ultimately benefit the Canadian dairy industry. In 2012-2013 Zoetis funded genotyping of approximately 2,000 Canadian proven sires so that their offspring could be included in the genome pool.  The addition of this genetic information will aid in the predictive value of genomic testing, in particular for Canadian only traits, such as temperament and milking speed.”

ZOETIS + SEMEX + HOLSTEIN CANADA + CDN – Combined Strengths. Collaborative Approach.

Effective May 1, 2012, Zoetis (formerly Pfizer Animal Health) joined the existing alliance between the Canadian Dairy Network (CDN), the Holstein Association of Canada (Holstein Canada), and the Semex Alliance (Semex).  Dr. Chan describes the strategy. “The intent of this alliance is to foster a collaborative approach to delivering predictive genetic information to the Canadian dairy industry, to promote female genotyping and to assist Canada’s dairy producers in using genetic information to make sound management decisions and propagate desired traits. “The members of the alliance feel that by engaging in this partnership, breeders ultimately benefit from the combined strengths of each organization.”

Update on Pilot Study Results

Dr. Josh Lindenbach, Warman Saskatchewan, a Clarifide Approved Veterinarian, shared some of the economic analyses that he did with two of the Zoetis pilot-project herds.  In both herds, Dr. Lindenbach sorted the animals based on LPI and compared it to kg of BF shipped.  “In Herd #1, there was a $960 average gross profit advantage between the top 1/3 and bottom 1/3 of the herd based on LPI (48 animals genotyped).  In Herd #2, there was a $1345 average gross profit advantage between animals that had an above average LPI number vs. a below average LPI number.”


Zoetis has received the following comments from breeders and vets involved in the CLARIFIDE program:

  •  “This gives us a better way to manage the heifer inventory by knowing which ones to keep, sell or use as recips, and which ones to use sexed semen on.”
  • “Herd weaknesses were known before but now we find them younger and more accurately“
  • “We are now buying semen from bulls that address herd weaknesses as identified by genomics”
  • “More targeted use of sexed semen”
  • “We have more open discussions of breeding discussions involving both vets and AI reps, sometimes even together!”
  • “By culling my bottom end heifers, the heifers coming into the milking herd are more solid producing animals. We have higher milk production and have been able to raise the overall health level of our herd.”
  • “It’s not the top half of my herd that I ever have to worry about – it’s the bottom half.  I want to be able to know ahead of time who could potentially cause me problems and be able to manage my heifer inventory appropriately, based on this knowledge.”


There have been interesting results from three different groups from the Zoetis field trial as Dr. Chan reports. “Breeders that are in the top 10% ,from a farm management standpoint, who are excellent at raising calves and keeping them alive, have reached a plateau with their production and are looking for the “next thing” that they can improve on to help them become more profitable were the first ones to trust in genomic technology and see its value.  Dr. Chan states, “The key is to make sure you have invested fully in your calf raising program to ensure that disease issues are kept to a minimum and calves have doubled their birth weight at 56 days – then you can be assured that these heifers will reach their full genetic potential.” She continues with the benefits for two other groups.”Breeders that are sitting on excess heifers and looking at their expenses were also quick to jump on board.  For a group of Hutterite breeders that are limited to the use of natural service bulls only, genomics provided them with an opportunity to push their genetic progress by culling some of the bottom end animals and replacing them with purchased animals that ranked higher on LPI.”  Using data that CDN supplied, Dr. Chan in 2012 looked at phenotype vs. genotype.  “We took the CDN database as being “one herd” and took the raw data without adjusting for any environmental effects.  Despite that, we were still able to show a significant difference in performance, if we used genomics as a predictor for performance.”

zoetis chart

The Bullvine Bottom Line

This sounds like every breeder’s dream.  It checks off several breeder, service provider and advisor goals. “Now breeders not only know a heifer’s genetic potential early in her life but have the information to find more accurate ways to allocate resources.”  Whenever the tools advance dairy breeders` goals and profitability, that’s a win-win for everybody.


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We are so used to leaving voice messages it can only be a matter of time until you hear.

 “Good morning Boss. I will be away from the milking line today.  If this is an emergency, please check with the veterinarian or better yet – find out why more than eight diseases are going through the barn? Have a great day. Cownt Me Out!

“It’s a Wake-Up Call for the Dairy Industry”

Regardless of how you receive the message about dairy health issues, there is no question that we have already received the wake-up call.  Whenever CowntMEout and her peers are fighting health issues, they are still in the lineup and could be having a negative ripple effect because they are contagious, costing money for treatment and losing money because of lowered production. You may laugh off the “cow calling” app on your smart phone, but disease is no laughing matter.  The incidence of disease in dairy cattle is increasing. So far the only way to tackle it has been through management practices and veterinary inputs. At least that’s where our thinking has been.  It’s time to pick up the phone!

Disease has your barn number. It’s going to call back often!

There is no acceptable level of poor health and, like telemarketing calls, you will receive many visits, at inconvenient times and with increasing frustration.  The higher incidence of health problems has risen side by side with the increase in milk yield, which has been sought after and achieved over several decades. However, along with poor health, increased lactation progress has been accompanied by reproduction problems and declining longevity. As if that wasn’t a big enough hurdle, there is also a genetic one. There is clear evidence that negative genetic correlations exist between milk yield and fertility and between milk yield and production diseases.  In other words, if selection for production continues unchanged, fertility, health and profitability are going to be put “on hold” permanently.

The Health Games.  Sick is costly. Health isn’t free.

As long as our cows continue to function by producing milk, we may be willing to live in denial of health issues.  Unfortunately, the list is growing well beyond the number one which is mastitis and includes: displaced abomasums; ketosis; milk fever; retained placenta; metritis; cystic ovaries; and lameness.  What is the incidence of each of these in your herd?  Do you keep records on all of them? We know from our personal health that you can’t fix what you don’t admit is a problem.  Those tiny signs add up until “out of nowhere” there is a health crisis.  That doesn’t work for people and it doesn’t work for bovines either.

Bad Prescription. “Take 2 Bales of Hay and Call Me in the Morning!!”

Don’t you just hate it when your doctor takes a laid back approach to your serious medical concerns?  Or does that feel like a reprieve?  You don’t have to fix what you don’t acknowledge.  Or does it boil down to who has the best answer?  The vet. The nutritionist.  Your neighbour.  It probably takes all three but we really need to pull back and start answering the questions about improved health even before mating decisions are made. Huge strides have been made in dairy breeding with the implementation of genomics. DNA analysis has only touched the tip of the iceberg for what is possible in analyzing dairy genetics.  This brings your genetics provider (A.I.) onto the health team. All that is needed is the will to change.

What can we do about it? Monitoring. Managing. Action.

You can hire someone to take care of sick animals.  You can pay for medication and extra care. Or you can decide to start with genetics and try to raise the genetic health level of your herd. All of these approaches start with the same first step.  You must monitor your animals and have detailed data on where, what, when and how health issues are affecting your dairy operation.

The hardest concept when dealing with health is that preventive measures are far better and less costly in the long run than the prescription, medicine and professional caregiver route. There needs to be more preventive action taken at the breeding stage.  Here is the first line of defence to reduce the diseases that lurk within genetic code and impact profitability now and for future generations of your herd.

The most crucial first step is to have accurate data. Good complete data that accurately identifies what is happening in the herd.  The information needs to be recorded and accurate before the cow is culled from the herd.  Dr. Kent Weigel, Extension Genetics Specialist, University of Wisconsin notes. “Current reports often don’t provide enough details to identify exact reasons why cows are culled. Animals can be recorded as ‘died,’ ‘sold for dairy,’ or ‘sold for beef,’ because of low production, mastitis infertility and so on. From that data, you might conclude that mastitis and infertility are the most common causes of culling on dairy farms. However, reported reasons for disposal can be misleading when one attempts to compare the management level of various dairy farms or to draw conclusions about the genetic merit of certain animals or sire families. Furthermore, once culled, that animal will no longer contribute information to genetic evaluations.  In effect, by culling time the most important source of health data has been eliminated.”

An ounce of Genetics is Worth Pounds of Cure?

As a result of research he has taken part in, Weigel says producers should not just consider the pounds of milk a cow produces as they weigh their decision about genetic traits.
You want cows that produce a live calf without assistance, cycle normally, show visible heat and conceive when they’re inseminated. Many cows fail to complete these and other important tasks because they have left the herd prematurely.” Weigel went on to say that some animals are culled for “multiple offenses,” such as difficult calving followed by ketosis and a displaced abomasum.  “She may then fail to breed back in a timely manner and be culled when her daily milk production falls below a profitable level,” Weigel says. “The farmer might code here as ‘sold for low production’ or infertility or disease. The reported reason for disposal is often a vague indicator of the actual problem.”

Get the Code – Fill the Prescription

Given the unfavorable genetic relationships between milk production and welfare indicators, the most effective route to stop the decline or even improve dairy cows’ welfare is by developing and adopting a selection index in which welfare related traits are included and appropriately weighted.

At a recent CDN (Canadian Dairy Network) open industry meeting, more than one presenter spoke on the genetics of disease and health. The proposed response to this complex topic is to develop one index that incorporates targeted health indicators.  We see the logic that cattle who have less mastitis or and lower somatic cell scores represent healthier animals in the herd. Until actual DNA snips are identified for specific health issues and diseases, an index that combines  SCC (somatic cell score) with fore udder attachment, udder depth and body condition score to produce the newly developed MRI (Mastitis Resistance Index) will take selection for healthier animals to a higher level.  The quantity and quality of the data contributing to these indices is key to how effectively they will identify sires with the healthiest genetics.  Isn`t it great that breeders, researchers and genetics providers are working together to move beyond the obvious.

Predict the Disease Proof by Building on What We Know Already

DNA markers for economically important traits could quantify the differences and be used to justify selection decisions on young animals with reasonable accuracy.

Short term, breeding organizations are urged to use available records to include fertility, health and longevity in a selection index in which greater emphasis should be placed on all fitness related traits relative to production traits. Genetic evaluations for health should complement and not replace genetic evaluations for yield.

“The udder is always the place to start evaluating a cow,” Weigel says. “Poor udder traits are the biggest problem, followed by poor feet and leg traits. Naturally, cows that avoid mastitis or injury to their udder are going to be in the dairy herd longer.” The major advantages of the genetic improvement for any trait are that changes are cumulative, permanent and cost-effective.

Who Will Answer the Call First?

Ultimately, the successful dairy industry of the future will maintain the gains made in milk production and make equal strides in the identification of healthy cattle. Whether it’s by choice or necessity remains to be seen. It will take everyone contributing accurate data.  The breakthroughs in production were made possible by tremendous amount of supporting data. To make similar progress in fighting dairy diseases, the same cooperation in building a database will be needed. Currently in Canada only 4 in 10 herds are participating in the capture of data on the 8 production limiting diseases.  In some European countries there is a database of mandatory disease recording that spans more than 30 years.

The Bottom Line

Some will write off the concerns raised here as over dramatic.  After all, personifying your cows as phoning in sick is beyond belief.  We all know that 21st Century contented healthy cows won`t phone in. They’ll text: “Guess what Boss? I’m healthy and I’m pregnant!”

The ones who are prepared for that call will be laughing all the way to the bank.


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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


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.





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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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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