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Archive for Inbreeding

The Truth about Inbreeding

Thursday, October 30th, 2014

Should breeders be concerned about the increasing rate of inbreeding in today’s dairy cattle?  Articles are regularly published about the need to lower the rates of inbreeding by such means as cross-breeding. However for purebred breeders planning to remain competitive in advancing their herds genetically, to increase the inventory value of their herds and to maximize the profit from their dairy operations, the matter of increased rates of inbreeding is more than a single item issue.

Breeder Attention to Inbreeding is Limited.

As I follow breeders’ comments on The Milk House (link) and other Facebook posts, I see little breeder concern or perhaps even awareness of any negative impact from focusing on a limited number of bloodlines that are more inbred than the general population.

Showmen often identify Atwood, a Goldwyn son, as the next great sire to follow Goldwyn as the Holstein breed champion in the show ring. Already, before they even receive their first official daughter proofs in December, I hear breeders talking about the attributes, including breed leading TPIs or LPIs of the many daughters they already have in their herds from two unproven bulls, Mogal and Uno. Supersire may not receive an official proof in December but, in time, all three of these sires will enter into the club of very, very extensively used sires that will lead to a further narrowing of the global diversity of Holsteins. That is what happened with Elevation, Astronaut, Blackstar, Shottle, Goldwyn, Planet and Oman in the past.

The Question is ……

Dairy breeders need to be asking themselves “How do I balance genetic improvement, dairy enterprise profit and increasing rates of inbreeding as I mate my herd?”  

What is Inbreeding?

In simplest terms, inbreeding is the mating of related animals. The more closely a bull and cow are related, the higher the frequency that their common genes will be passed on to their resulting progeny. Animals that do not meet the breeding goals of breeders do not get the opportunity to have their genes passed on. As a result, the genetic diversity of the population decreases. In short, focused selection contributes significantly to decreased diversity. It is a double-edged sword.

Varying Degrees of Inbreeding.

The Dairy Cattle Reproduction Council (a proactive organization of professionals interested in enhancing reproduction through technology) has produced the following helpful chart to demonstrate the varying degrees of inbreeding.

Varying Degrees of Inbreeding

Some interesting facts can be extrapolated from this chart. Line breeding has been used by dairy cattle breeders to fix the good genes in their herds. But it can also accentuate any negatives associated with the breeding lines used. Selection within a breed has, by far, been the tool of choice for genetic improvement especially since the introduction of artificial insemination. Its contribution to increasing rates of inbreeding has come through the very extensive use of the top sires. Inbred crosses within species has been promoted by some as a solution to the increasing rates of inbreeding but very often the benefits quoted are for single traits and not for total lifetime profit of the resulting generations.

Level of Inbreeding

For North American Holsteins from 1960 to 2010, the levels of inbreeding have gone from zero to 7% to 8%. Moreover, it is continuing to increase at about 0.3% per year.

Genetic Diversity and Inbreeding Article - September 2014-3

Impact of Inbreeding in Dollar Terms

Based on USA studies it is estimated that for each 1% increase in inbreeding there is a loss in lifetime net income of $23.11. That equates to a difference of $96.44 for a 9% inbred cow compared to a 5% inbred cow. Canadian and Irish crossbreeding studies show slight lactation losses for milk, fat, and protein yields, but gains for fertility and health traits when breed crossing is practiced. However, neither study reports a net lifetime profit figure comparing breeding pure to crossing breeds.

The question when making a mating decision comes down to correcting for the loss due to inbreeding between the sires under consideration. A sire with an Inbreeding Coefficient of 8% would need to have a NM$ value of about $70 more than a sire with 5% Inbreeding Coefficient for them to be considered equal.

It is more than looking at the Inbreeding Coefficient (IC)

An animals IC tells the degree to which the animal is inbred. However in breeding it is the degree to which the progeny of a mating is inbred that needs to be considered. That means that a sire will not likely produce calves with similar ICs for every mating in your herd. It all depends on a sire’s varying degrees of relationship with your females.

In the USA and Canada information is provided for every sire on how he will mate with the national population of females as to inbreeding level. In the USA the terms used in Effective Future Inbreeding (EFI) and Genomic Future Inbreeding (GFI), while in Canada the term used is Relationship Percent (%R). In all cases, they are general guides to which sires will produce more or less inbred progeny.

What is the Ideal?

The are no perfect numbers for EFI, GFI or %R. It depends on both the genetic merit and inbreeding percent of the resulting progeny. Generally speaking, EFIs and GFIs over 10.0% and %R over 15% of the progeny should be avoided by using an alternate sire that is less related to the dam.

Sound Advice

Dr. Nate Zwald of Alta Genetics provides two thoughts relative to inbreeding:

  • Will the use of genomic sires speed up the rate of inbreeding? – “Yes on a breed level it will, but we are also increasing the rate of genetic gain in an incredible way. So our goal should not be a ‘less inbred’ cow but, instead, the most profitable cow. Over the past 25 years, we have created more inbreeding but also more profit. The same is true now with genomics, except that we should now expect both inbreeding and genetic gain to increase at a rate two to three times what we experienced in the past.”
  • Does this mean we can soon expect to get to 10 percent inbreeding level on a breed-wide basis? “Yes says Zwald. Geneticists are working on ways to balance the inbreeding level with genetic gain on a breed-wide basis, as a producer you should only be concerned with inbreeding versus genetic gain in your own herd.”

Ways to Select Bulls to Use in Your Herd

In summary, there are basically three ways to address both genetic gain and increased inbreeding:

  1. Use Outcross Sires that are low for EFI, GFI or %R. (Read more: 12 Outcross Sires to help Control Inbreeding)
  2. Use a herd mating program that takes into consideration inbreeding. Most AI studs have such a service.
  3. Use sires that optimize your breeding program that are not closely related to your herd (i.e. GFI below 10% or %R below 16%) (Read more: What’s the plan?)

The Bullvine Bottom Line

As long as breeders plan to rapidly increase the genetic merit of their herds an increasing rate of inbreeding will be with us. Remember when mating a cow and bull it is the genetic merit and inbreeding percent of the resulting progeny that is the focus and not the parents’ values. One breeding program will not suit every breeder, but basing decisions on profit should be part of every plan.

The Dairy Breeders No BS Guide to Genomics


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Stop Talking About Inbreeding…

Tuesday, March 25th, 2014

Dairy cattle breeders talk about attempting to keep the level of inbreeding within check in their herds. Poultry, swine and corn breeders talk in terms of inbreeding and producing lines and then crossing the inbred lines to produce the birds, piglets and seeds that are used for commercial production. In beef, breeds have been developed for their specialities and then breeds are crossed to produce the commercial animals. The challenge currently being faced by Holstein breeders is that once again the level of inbreeding is creeping up and that has the potential to be a limiting factor when it comes to on-farm profit. Let’s look at where the level of inbreeding is at and how breeders might address that.

Current Inbreeding Levels

Dr. Filippo Miglior, Canadian Dairy Network, presenting at the February 2014 Advancing Dairy Cattle Genetics Workshop held in Phoenix Arizona,  reported of the state on inbreeding in Holsteins born between 1982 and 2012..

MIGLIOR - Tempe Meeting Feb 2014 - Genetic Diversity and Inbreeding-17

It should be concerning to breeders that over the most recent time period, 2007 to 2012, that the Inbreeding Coefficients for Holsteins everywhere, North America and Global, increased at the rate of 0.36% and 0.33% per year respectively. These levels are the highest in modern Holstein breeding history.  Levels four to almost seven times large in 2012 compared to 1982 should be a wake-up call for our industry. The inbreeding levels from 1987 to 1997 were a concern back then when only a few sires were being used to produce sons for A.I. progeny testing programs. Breeders and A.I. took the warnings seriously and increased the number and diversity of sires of sons entering A.I.

What Has Been Happening?

There are a number of factors that need consideration.

Limited Number of Bloodlines Where once the bloodlines often had country or regional focus, Holstein breeding has gone global with only a few total merit indexes in use and TPI dominating. Diverse breeding resulting from the environmental situation or the cheese produced has disminished.

The number of different bloodlines used by A.I. companies has been greatly reduced. The table below is a global report on the Top 20 Sires of Sons since 1986. Half of these sires were born and used prior 2000. However recent sires like Man-O-Man, Planet, Shottle and Superstition are in the top ten. Only one of these sires, Shottle, was first proven outside North America but his pedigree was from North America. The end result is that this extreme use of a limited number of sires of A.I. sons has contributed to the increased inbreeding in the past 25 years.

MIGLIOR - Tempe Meeting Feb 2014 - Genetic Diversity and Inbreeding-20

Rapid Genetic Progress The significant increases in inbreeding comes about as a result of the very significant increase in the past decade in the genetic merit of the Holstein breed. The following graph produced by USDA shows the change in the annual rate of genetic improvement for Net Merit. This change was a result of intense selection  and increased accuracy using genomic information. However the fallout from that is the greatly increased inbreeding that we have now.

MIGLIOR - Tempe Meeting Feb 2014 - Genetic Diversity and Inbreeding-4

Adjusting Indexes for InbreedingUSDA/CDCB has produced reports on adjusting US production indexes for level of inbreeding. There is much more work to be done on the effects of inbreeding beyond milk production. The truth is that it will take a long time to determine adjustments for traits relating to health and fertility. Note that the field observations for those areas are likely only available in the Nordic countries.

Limited Number of Sires of Sons The two graphs below show just how short the list of sires of sons has become during. Having only 16 to 19 sires producing 50% of the young sires entering A.I. was great for genetic gain but for inbreeding it was a recipe for major problems. Even in 2011 there was still too much focus on too few sires of sons when only 32 produced half the young bulls entering A.I.

MIGLIOR - Tempe Meeting Feb 2014 - Genetic Diversity and Inbreeding-11

MIGLIOR - Tempe Meeting Feb 2014 - Genetic Diversity and Inbreeding-13

Focus is on Top Genomic AnimalsBreeders should be concerned about inbreeding with the extreme focus on only the very top young heifers and bulls. This has also put downward pressure on animal values for high indexing animals that are just outside the top group. Genetic gain for production and type could be almost as good if there was increased selection pressure for other economically important traits. Remember that the very top heifers are full sisters to the young bulls entering A.I. Where is the genetic diversity in that?

Inbreeding of Sire List ToppersThe Bullvine has studied the Expected Future Inbreeding (EFI) for the top forty Net Merit Dollars ($NM) sires on both the Holstein USA Dec ’13 proven and genomic sire lists. Each 1 percent increase in EFI reduces milk proofs by 65.3 pounds. The published proof on a bull with an EFI of 4 per cent would be reduced by 261 pounds (4 X 65.3 = 261).  The top 40 proven $NM sires have an average EFI 6.4, the genomic test sires also had an average EFI of 6.4 (Note: Had to be active with NAAB).  Sires with O-Man blood all have high EFI’s due to O-Man’s extensive use as a sire of sons.  Interesting to note that while both the top proven sires and genomic test sires average the same, this is a far greater range in the proven sires, the lowest proven sire in the top 40, Twist, has an EFI of 5.5, and the highest EFI proven sire in the top 40, Manifold, has an EFI of 7.  In the genomic test sires, the lowest EFI, (Rubicon, Mr Max and Magoo all tied at 6), and the highest EFI belongs to Dozer at 6.7.

Breeders looking for the sires with the lowest expected future inbreeding should look up:

 Proven Sires

Erdman – Kings-Ransom Erdman Cri-ET – 01HO09800Kings-Ransom Erdman Cri Twist – Clear-Echo Nifty Twist-ET – 029HO14335Clear-Echo Nifty Twist
AltaNetworth – Bomaz AltaNetworth-ET – 011HO10767Bomaz AltaNetworth Dorcy – Coyne-Farms Dorcy-ET – 029HO14142Coyne-Farms Dorcy

Genomic Test Sires

Rubicon – Edg Rubicon-ET 151HO00681Edg Rubicon2 Mr Max – Bomaz Mr Max-ET – 151HO00675Bomaz Mr Max
Magoo – Bomaz Magoo-ET – 151HO00677Bomaz Magoo Troy – River-Bridge Co-Op Troy-ET – 001HO11056River-Bridge Co-Op Troy

Polled not likely to help lower InbreedingWith more breeders breeding for polled animals, some of us may have thought there could be genetic diversity brought into Holsteins by this route. Well that just isn’t so. What is happening is that the same all too frequently used sires in horned are showing up as the sires or maternal grandsires in polled. The only outcrosses in the polled young sire pedigrees are the generation of sires or dams that introduced the polled gene.

What Needs to Happen?

The Bullvine offers the following ideas for how to make progress to reducing or at least holding the inbreeding levels.

Calculate Inbreeding Levels for Every CalfRemember that it is the inbreeding level for the calf that is to be born that needs to be watched. To achieve a reduction in inbreeding, the sire and dam should not be closely related. A good example where the breeder did his homework is Crackholm Fever, 6.35% inbred. His parents are more inbred than he is but they are from quite different lineage. His sire Goldwyn (James x Storm x Aerostar) is 15.17% inbreed while his dam Fashion (Blitz x Mattie G x Rudolph) is 8.17% inbred. Inbreeding can be managed. Most sire mating services have incorporated the minimization of inbreeding into their programs.

New Total Merit Indexes At the present time total merit indexes in the United States (TPI and NM$) and Canada (LPI) are under review for updating to include additional economically important heritable traits for which data is captured. Breeders need to have input into the further development of those indexes. Once those indexes are revised, new males and females will come onto the elite lists. Those animals are likely to bring forward the opportunity for breeders to use them to both generate more on-farm profit and to reduce inbreeding.

Develop Lines within Holsteins A.I. companies have already started to develop lines that place emphasis on traits like health and fertility. No doubt lines will be developed for feed efficiency, once more is known about it. Having such lines available will give breeders the opportunity to specialize the families on their farms or to cross lines to end up with less inbred animals. It could make for the best of both worlds – for the breeders and for the A.I.

More Study of the Genome As more and more animals are genomically tested there will be more accuracy to genomic results. But it does not end there. By studying each animal’s genome, it will be possible to know the exact level of inbreeding instead of what is currently done, which is only an estimation based on parentage. This will provide for yet another way to help tackle the inbreeding issue. Definitely genomically testing all heifers in a herd will, in the future, have a multitude of benefits for breeders (Read more: Herd Health, Management, Genetics and Pilot Projects: A Closer Look at ZOETIS)

The Bullvine Bottom Line

Holstein breeders and the breed cannot afford to fiddle while Rome burns when it comes to inbreeding. It is time to take action to reduce inbreeding levels. It does require collective action by the breed, on behalf of breeders and A.I. companies. It is not too late to act. The time for procrastination has past.



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Many articles and various approaches have been written over the past couple of years on how to deal with inbreeding in dairy cattle (Read more: 20 Things Every Dairy Breeder Should Know About Inbreeding and INBREEDING: Does Genomics Affect the Balancing Act?). However the herd breeding approach towards inbreeding that is best suited for individual dairymen is not a one size fits all.


Frequently the method recommended is to find out-cross sires and to use them on a herd rather than closely related or inbred sires. The Bullvine produced such a list a few months back (Read more: 12 Sires to Use in Order to Reduce Inbreeding). However totally out-cross sires are almost non-existent as very few Holstein A.I. breeding bulls do not contain, in their first three generations, a cross to, at least, one of Bolton, Blitz, Durham, Goldwyn, Oman, Planet, or Shottle.

Sires From the Past

But we should not despair. This problem has been the same challenge for the past century. In the past there were concerns about too much concentration of the Holstein bloodlines when Rudolph, Blackstar, Valiant, Elevation, Astronaut, Rockman, the Burkes and the Montvics were in their hay days. It is not new in 2013. A few years back Holstein International produced an article on the extreme focus, around the world, on Blackstar as he had a few hundred sons that were sampled in A.I. But we moved on past the Blackstar focus and outcross sires came along and saved the breed from a one sire focus.

Recent Out-Crosses

The most recent ‘heroes’ to assist with avoiding inbreeding Holsteins have been Shottle, Oman and Planet. They themselves have average to below average inbreeding percentages – 6.25%, 5.06% & 7.27% respectively. We must remember that it was not their lower inbreeding percentages that attracted breeders to them it was what their daughters could do in every breeder’s herd. They were all out-crosses when they arrived on the scene. However, they were all used heavily, perhaps too heavily. In fact it is not the bulls that are the problem. It is our over abundant use of sires on close relatives that lead to them becoming inbreeding concerns.

Why Inbreeding was Practiced in the Past

Before the era of genetic evaluations, inbreeding was employed in what was called ‘Line Breeding’. The concept was to find a family that had the attributes a breeder wanted and then to double, triple or even quadruple up the cow or bull in the pedigree of the next generations. Breeders persist in using the line breeding approach even though we now have very accurate genetic indexes. As a result we are creating an inbreeding problem for ourselves. Especially for traits like fertility, immunity, vigour and longevity. In 2013 these traits are coming to the forefront in the breeding of dairy cattle.

What is Average for Inbreeding?

In the USA inbreeding is expressed by a term called Inbreeding Coefficient, whereas in Canada it is called Inbreeding Percent. The average value for each appear to be similar with the average inbreeding in Holsteins in Canada being 5.87% in 2009.

Here are some examples of inbreeding percent that can be expected from within family matings:

  • Brother- Sister     25%
  • Half Brother – Half Sister   12.5%
  • First Cousins    6.25%
  • Second Cousins    3.13%

In other words, the average animal in the Canadian Holstein populations was almost equivalent to being the result of mating first cousins.

Sire Selection & Inbreeding

Choosing sires to minimize inbreeding is not as simple as going to or and finding the top (lowest) bull for inbreeding percentage or inbreeding coefficient. Thus eliminating from your breeding program any bull that is over average for inbreeding. You must also consider the bloodlines in your herd and the inbreeding of your females.

It can happen that a cow and a bull each have low inbreeding percents but due to being from similar bloodlines the resulting progeny are inbred. Take Goldwyn for example. His sire, James, has an inbreeding percent of 3.67%. His dam, Baler Twine’s value is 9.74%. Yet when mated because of the intense line breeding to both Grand and Aerostar, Goldwyn’s inbreeding value is 15.69%. The line breeding did allow for his genetic make-up to be homozygous at many loci. We all know how he stamps out show type. However breeders planning to line breed further with Goldwyn in the pedigree should be concerned about the definite possibility of inbreeding depression for health and fertility traits. Sire stack does not show inbreeding as accurately as inbreeding coefficient or percent does.

For breeders interested in some bulls with below average inbreeding values, The Bullvine offers the following lists. Note that we have chosen bulls with high total merit indexes and above average for Daughter Pregnancy Rate and Daughter Fertility. There is no benefit to using a sire that has a low inbreeding number yet produces daughters that have low fertility or are lacking in any of healthy fast growing calves, immune animals, SCS, Feet & Legs or Mammary System. Of course the lack of heifer information across herds could be our Achilles Heel in the not too distant future in genetically advancing our heifers.

Tables 1 – Top Sires with Lower Inbreeding Levels

NameInbreedingIndexFatProteinUDC/MSFLC/F&LSCSDPR/DFNet MeritSire Stack
USA Sires
Amighetti Numero Uno3.62456 (GPA TPI)89472.72.212.591.3836Man-O-Man x Shottle x
Co-op O-Style Oman Just4.12246 (GTPI)47561.212.112.712.4728Oman x Teamster x
Farnear-TBR-BH Cashcoin52470 (GPA TPI)78522.881.242.561.4904Observer x Goldwyn x Shottle
De-Su Observer5.52332 (GTPI)61523.020.892.760.6792Planet x Oman x BW Marshall
Canadian Sires
Regan-ALH Diplomat5.342905 (GPLI)49738102.81101327Mr Burns x Oman x Durham
UFM-DUBS AltaEsquire5.692864 (GLPI)11063142.79103466Oman x Sam x Patron
Genervations Lexor5.793291 (GPA LPI)908411142.89100652Man-O-Man x Goldwyn x Durham
Swissbec Brekem5.853227 (GPA LPI)728013102.87102641Bookem x Man-O-Man x Mr Burns
Other Sires
O-Man End-Story3.812915 (Mace LPI)8069673.13103483Oman x Besn x Luke
Bertaiola Mincio4.32927 (Mace LPI)744516113.06100460Bolton x Iron x Mtoto
Koepon AltaClassman5.293180 (Mace LPI)94738102.71103721Man-O-Man Shottle x Aerostar
KNS Reminder5.743199 (Mace LPI)106797102.86101681Sudan x Oam-O-Man x Goldwyn

The Bullvine cautions breeders using genomic sires to not use just one sire. Many of the top sires on the genomic listings have average to above average inbreeding numbers. So it is best to use many genomic sires. Many breeders wisely use from 5 to 20 doses of a genomic sire and then move to another high genomic sire.

Six Suggested Practices

  1. Avoid using any sire that has above average inbreeding numbers especially if his pedigree has similar sires to the females in your herd.
  2. After identifying sires with average to below average inbreeding numbers, make sure they are superior for traits important in your breeding program like fat yield, protein yield, feet & legs, mammary system, udder health and fertility.
  3. Use a sire’s genetic and inbreeding indexes when selecting sires and do not practise line breeding.
  4. If there is a sire that you would like to use but his inbreeding index is on the higher side then use his top two non-inbred genomics sons.
  5. Use computerized sire mating programs as they consider inbreeding when making sire recommendations.
  6. A.I. organizations should publish the inbreeding values for the sires they sample, prove and market.

The Bullvine Bottom Line

Inbreeding is a consideration but not the driving force when it comes to improving the genetic merit of a dairy herd. Line breeding served its purpose in the past but now can be detrimental to lowering inbreeding in dairy cattle. By following the suggested practices you will not only be able to better understand inbreeding, you will actually accelerate you genetic advancement, by not avoiding those sires that you thought would have been a inbreeding problem.  It’s important to remember just how much effect inbreeding will have, and how does that compare to the difference in genetic merit between the sires you are choosing from.

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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