Thursday, June 1, 2017

BIF 2017: What the beef industry can learn about genomics from other industries

Tom Lawlor
Holstein Association USA

Lawlor cited Jerry Taylor's article saying that Holsteins are the genomic prediction poster cows. Genotyping has increased and genetic improvement has increased in the dairy industry.

But, not everyone is happy. From The Bullvine website:

  • "How Genomics is killing the dairy breeding industry"
  • "What the Experts Won't Tell You About The Future of the A.I. Industry"


The dairy industry has had to change their data structures and analysis methods. Everyone in the dairy industry is winning, but some breeders are winning more than others.

The Holstein breed is rapidly turning over their population and seeing more profitable animals.

Genomics also allows them to look at genetic merit, inbreeding, undesirable genetic defects, and breed composition.

One in five animals are expected to be a carrier of a genetic defect causing early embryonic loss. We have to abandon our old beliefs about not using animals with genetic defects. These are at too high a frequency in the population to not use carriers. What is required is getting the information out for breeders to use. They specifically call them haplotypes, e.g. HH0, HH1, etc., is to allow marketing of these animals.

The Holstien bull Storm's best chromosome is chromosome 11 inherited from his dam. However, this chromosome 11 also carries the Haplotype associated with Cholesterol Deficiency (HCD). Breeders still need to use this bull, but they need to work to create descendants that don't carry HCD.

Holstein breeders are doing this! They are much more likely to breed a non-carrier cow to a carrier bull. They are working to blend the best genetics while also systematic and methodically removing genetic defects.

In the German Holstein industry, in 2011 10% of their matings used genomic bulls (young bulls with genomics). By 2015 that percentage was up to 30%.

S-S-I Partyrock Profit-ET has 5 generations of ancestors that have been genotyped. Very aggressive use of the technology to make improvement.

Breeders were looking across the world for the best genetics. But, with genomics, there is more emphasis on developing the best genetics in the world. Top sires now have most of their ancestors being owned and breed by a single farm. The best Holstein genetics are now coming almost exclusively from the United States.

Registration of offspring of the bulls from companies with an aggressive genomic program increased 16%. These companies have great market share. Companies are doing this by controlling access to their top genetics. They have pre-release semen, early access to the top young bulls is being limited to a "select group". If a bull is born from one of these matings, the company has first right to this bull. Once the bull is released, most of the semen sold is for female selected sex-sorted semen. This is great for commercial producers, because then can make sure they have the best females.

This is also used as a limitation of competitors access to a company's best genetics. However, this has not been effective, as a bull's top son's often come after the pre-release period is over.

There are also "Free Agents". These are bulls with high genomic profiles, but no contract on that bull.

AI stud ownership of female genetics is now common.

The dairy industry has seen growth of large National Genetic Evaluations, there has been a move away from the Interbull model of "pooling data".  If you contribute phenotypic data, you pay $15 for a genomic evaluation of a bull calf. If you are not contributing phenotypic data, you pay $150 for a genomic evaluation of a bull calf. Typically for AI service the fee is $575. If it comes from a third party, the cost is $1200.

Only the best cows have been DNA tested for genomic-enhanced predictions. This can cause a bias in the prediction. Single-step removes the bias that comes from only the best cows being genotyped.

How do you invert a matrix that is 760,000 by 760,000? You don't. You use the APY method. This method selects a core group of animals, say 15,000 animals. You invert this 15,000 by 15,000 matrix and use it in a recursive method.

The United States needed a commercial entity to do genetic evaluations. Genetic predictions moved from the USDA to CDCB.

There has also lead to fragmentation of genetic evaluations. Zoetis, ABS Global, GENEX, and CDCB all have separate evaluations for health traits.

The big take home from Holstein genotyping, is not that they have done a lot, but that each year the rate of genotyping increases. This also allows an extra boost in improving the lowest heritable traits.

Lawlor sees a renaissance period in dairy breeding. There has been great improvement in health and other hard to measure traits.

The competition between breeds has increased. Holsteins and Jerseys have a stable outlook into the future. Other breeds may struggle to stay relevant. Do not be a beef breed that does not have a genomic evaluation!

Genomics also allows us to check breed ancestry. A top Jersey bull, FARIA BROTHERS RAWLS {2} was identified as 20% Holstein. Most of the top Jersey bulls have Holstein genetics 3 to 5 generations back.

With genomics, the dairy industry sees a larger gap between progressive and less progressive herds. Progressive herds are widening the gap.

The phrase used to be genetics program. The phrase is now "genomics program". Sire selection is key to this! Advanced reproductive technology, such as IVF, is essential to a genomics program. They are seeing on-farm IVF facilities and use of beef semen on bottom tier of dairy cows.

A cow's ability to make eggs for embryo transfer is now a trait of interest.

There is no set practice for the use of genomic testing in large herds, varies between 0 to 100%.

Imputation is very important.

They can identify differences between bulls that have consistent progeny and bulls that have more variable progeny. Consistent progeny is desirable in a commercial setting. More variable progeny is desirable in a seedstock setting in which you are striving for genetic improvement.
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