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Why we genomic test

Maria F. McGinnis Published on 31 December 2014
Genomic testing map

Some use it to increase marketability of show cattle, and for others, it’s used to determine production in a commercial herd. Regardless of the specific reason, genomic testing has been part of the dairy industry for more than five years and has proven effective with diverse dairies across the world.

Dr. Bennet Cassell, professor emeritus and renowned dairy geneticist from Virginia Tech, moderated a producer panel discussion at the 2014 World Dairy Expo in Madison, Wisconsin, to explore the different ways genomic data is being used to improve dairy herds.

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The panelists included the following dairymen:

  • Matthew Nuckols from Eastview Farm in Beaverdam, Virginia, milks 120 registered Holstein cows in partnership with his cousin, uncle and father. In total, Eastview Farms is home to more than 250 registered Holsteins. Two-thirds of the herd focuses on functional type using Total Production Index (TPI) and Net Merit to make breeding decisions. The other third of the herd is bred with a focus on show ring type. Eastview Farms has sold cattle to Japan, Italy, Germany, Spain, Mexico and Canada.
  • Greg Andersen from Seagull Bay Dairy in American Falls, Idaho, milks 600 cows in a family partnership. The farm is also home to an elite herd of more than 80 registered, high-type Holstein cows where genomic testing is used extensively. Seagull Bay Dairy achieved notable success, with the herd favorite, Ammon-Peachy Shauna, named the world’s leading genomic bull-dam.
  • Robert Bignami from Brentwood Farms in Orland, California, milks 1,600 registered Jersey cows and is known around the world for excellence in Jersey breeding. Together with his wife, Pam, the Bignamis are the breeders of the former No. 1 genomic Jersey Performance Index (JPI) cow and several No. 1 JPI sires. Bignami is an American Jersey Cattle Association (AJCA) Master Breeder award winner and former president of the AJCA.

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Why do you conduct genomic tests in your herd? How did you get started in genomic testing?

Nuckols: We used genomics to sort the herd and to determine the cattle we want to breed and market. We have found that the genotypic data tends to follow each animal’s phenotype. Several of the bull studs encouraged us to get involved in genomic testing early on.

Bignami: I was fortunate to study under Dr. Lee Baldwin (University of California – Davis), and back in the 1960s he started all of this, so when it became available, we wanted to get involved as soon as we could. Initially, we tested 1,000 head of cattle. We also tested every calf to see what we would get.

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Now we can sort who will give a high test based on what we have learned over the years. Fat and protein are highly repeatable characteristics in the test, and they need to be paired with functional type; otherwise, you will get cattle that can’t handle the production you have put in their bodies.

Andersen: We use genomic testing to identify desirable traits in our elite herd. We use it to identify the best donors, and we also use it to help with purchasing decisions. We use the data to mate the top females to top bulls in hopes that the resulting bull calves will be used in the A.I. industry.

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How do you justify the costs of genomic tests?

Nuckols: We currently test all females and now all males. The test is about $42.50 per animal through the Holstein Association, which is $4,500 per year. For us, the test is a no-brainer because we can quickly make up the cost by selling animals for higher prices. The test results help us make better decisions on which cows to flush, use as recipients or breed.

Bignami: Genomics is used to determine bull decisions in our herd – both within the farm and when we are looking to bring genetics into our herd. We test bull calves to determine who will be sent to A.I. That certainly makes up the investment in the test itself.

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Further, we test 30 to 60 of our best cows. Once we know the best cows, we feel better about investing in in vitro fertilization (IVF) and other technologies. We make initial decisions about which genetics to bring into the herd on pedigree and traits. From there, we use the test to determine the best bulls.

Andersen: We test about 40 to 60 animals per year, and we justify the cost because we focus on sending males into A.I. The tests also help us identify which animals to use our flush money on. Overall, we are able to make better breeding decisions, which leads to better marketing.

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How do you decide how much risk to take on new, high-genomic sires for A.I. use in you herd?

Nuckols: We are a relatively small herd, and we choose to spread our risk. We don’t use more than 10 units of any one bull. Our logic is that if you take the best bulls and fast-forward a few years, some bulls are going to go up and some are going to go down. Limiting the frequency of use helps us cover our risk.

Bignami: We use half proven bulls and the other half we use high-genomic bulls. We use about 10 genomic young sires per year, and we breed 2,000.

Andersen: It’s unfair to compare proven bulls with young sires based on the reliability discussion (increases with age), but that said, I don’t use any proven bulls. I select strictly on genomics and look at the top Net Merit and highest-protein bulls. We breed the top females with the top-genomic bulls focusing on high protein and health traits. We might use two to four genomic bulls very heavily.

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What have you learned? What works for you? What has not worked for you?

Nuckols: Type is very reliable, and our type has gone up. We have had very few misses, and before genomics, even with proven bulls, we couldn’t say that. We have learned that we need to make more of an effort to get to the high-genomic bulls sooner.

Bignami: Everything works when you have $29 milk, and nothing works when you have $14 milk. Seriously, though, we have learned that production data is valid. Forty percent of our daughters are by high-fat bulls and our milk is down a little, but our (fat) test is up half a percent.

Andersen: We have learned that the genomic predictions have gotten better over time. For me, genomics has changed how I look at animals. I used to place more weight on the pedigree and classification scores, and now I don’t look at that as much.

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How might genomics benefit commercial breeders? Should they pay for genomic tests on females, and if so, which ones?

Nuckols: Ideally, every animal would be tested. If a commercial dairy can make better breeding decisions, they will have better animals. Plus, the cost of the test is good for the life of the animal.

Andersen: The more animals that are genomic-tested and in the milking string, the more data we have.

Bignami: For a commercial dairy, there are two main reasons to use genomics: first, for sire selection; and second, if you test your best, you might be surprised at what you find and it might help the breed.

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Are there any disappointments that you want to share, and what is the future?

Bignami: We have had some heifers calve that milk like crazy and we know they are not going to last. In the future, it’s about the total package, and there will be a greater connection between what you see on paper and in your milking parlor.

Andersen: There have been some cattle that I wish would have turned out better than they did. In the future, I think there will be greater importance on production and health traits over linear type.

Nuckols: I’d like to see greater focus on feed efficiency and foot health. I’d also like to know the percentage that each parent is responsible for in the offspring. For disappointments, when we look at the list of the top 200 females, 180 of them are from 10 places. We need to see more farms rewarded.

The panel agreed that genomic data is getting better over time and is being used in different ways for diverse benefit. Overall, increased data means smarter breeding decisions, which leads to better and healthier cows. PD

Maria F. McGinnis is a freelance writer based in Sun Prairie, Wisconsin.

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