Genomics explained thanks to the American Guernsey Association

Genomics 101

Reprinted with permission from the August 2015 Guernsey Breeders’ Journal


By Cheri Oechsle, Managing Editor

Genomics –

What is it and what does it truly mean? Two questions most dairymen have been asking since the term ‘genomics’ appeared into the daily stream of dairy talk.

A seminar was conducted during the National Guernsey Convention in Walnut Creek that addressed this issue. Conducted by Chuck Sattler and Blaine Crosser of Select Sires, Inc., the two gentlemen set out to enlighten the obscurity of genomics. Here is a synopsis of their presentation.

Genomics is a tool, or a piece of information, added to the traditional methods of identifying true genetic merit. Sattler stated, “Progeny testing, DHI testing, pedigree information is all still important, but now we can DNA test when animals are young to get additional information to know if the animal inherited favorable genetics from their parent or not, helping to decide earlier on that animal’s future.”

In 2006 a company called Illumina developed the SNP-50 chip, a chip that allows testing for 50,000 markers in one assay (or animal) at an affordable cost. Prior to that only 50 markers could be run. With this technological breakthrough, it allows for the start of making sense of base pairs in the genetic information. Now, it has advanced to over 500,000 markers which is useful in research.


How we used to do it vs adding genomics

Previously, we assumed the pedigree information was 100% accurate, assuming that half of each calf’s DNA comes from parents and one-quarter then comes from the grandparents. On average, that assumption is not inaccurate – but on the individual basis, it is not as accurate as assumed.

The genomic pedigree information can now track an individual’s DNA more accurately. Chromosomes don’t always segregate as predicted. Genomic testing, provides information on what chromosomes, or pieces of chromosome got transmitted. Some of the grandparents’ chromosomes may or may not have transmitted as previously assumed. Genomics allows us to adjust the traditional genetic evaluations based on which parent/grandparent transmitted the DNA. The influence of each segment of chromosome on each trait can be quantified, keep in mind only 50,000 markers are revealed for each animal.

Genetic evaluations that include genomic information are more accurate for several reasons. Genomic testing makes it possible to verify that the recorded parents are correct. While the accuracy of the recorded parents for animals with traditional evaluations is high, it is not always 100%. As discussed above, improved accuracy also comes from being able track the contribution of DNA from each ancestor. Finally, with enough historical data, we can begin to estimate the influence each chromosome segment has on each trait and use this information to supplement the traditional genetic evaluations. As more cows and bulls are tested, the information will become more meaningful and accurate. As it gets into the marketplace and people start using the testing and providing more information, the reference populations will get better and information even more reliable.

“Genomics will help us select young bulls more accurately, not necessarily with sires that already have daughters,” said Crosser.  To date there are 2,333 Guernseys genotyped worldwide. Using male genotypes from all countries and female genotypes from U.S. cows, a test run has been completed to determine what improvement genomic data can have on reliabilities compared to the traditional parent averages used today. Based on the predictor group size compared to other breeds, a minimum of 3% to a maximum of 5% reliability increase was predicted. Analysis was done for five yield traits, three functional traits and 14 type traits. The reliability gain significantly exceeded predictions with a mean gain of 14.4%.

The genomic evaluation tool may mean breeding strategies need to be adjusted.Asking questions such as using young sires or daughter-proven sires as fathers for future AI sires or as AI bulls for breeding programs. Also – can we now, with genomics, use heifers or first-lactation cows as mothers for future AI sires? This can decrease the generational interval resulting in offspring out of young sires and young heifers with the use of IVF and genomic evaluations. It can also offer breeders the opportunity to market offspring earlier or determine which genetically superior animals to use for breeding stock, using genomic information along with the traditional information.

The next steps

As discussion in the seminar wrapped up, the challenge is presented for breeders to genotype females to increase the information available as well as the overall accuracy of reliability. The AGA has taken steps to become the nominator for breeders to be able to submit samples for testing. Two labs are currently available to run results, both are listed on the AGA website. As data becomes available, the information will be made available. A trial run of genomic test results is projected to take place with the August proofs based on the information gathered during the recent Guernsey Foundation Haplotype study. This information will be released to the owners of the animals in the study in August. In December a public genomics summary is projected to be released with information gathered to date.

For more information, contact the AGA.

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