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Genomics: How far have we come, how far can we go?

Donald Sanders Published on 23 May 2014

Recent scientific developments have opened up unprecedented opportunities to improve dairy cattle genetics … and production.

A friend and dairy client of mine, who has a noted, high genetic merit purebred herd, excitedly told me that these advances have turned the purebred dairy cow and genetics business upside-down. And, he believes, small-farm purebred operations will be less likely to fit into the future of genetic stock for the bull stud industry.

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It has only been a few years since scientists mapped for the first time ever the bovine genome – the DNA or blueprint of the genetic material that makes a cow a cow. This has made it possible for the bull stud industry to identify cows with superior genetics and then mate them to bulls with similar genetic traits.

This capability was made possible by the work of USDA scientist Curtis Van Tessell and his colleagues. He developed a test for cows – the single nucleotide polymorphism, or SNP, test – that detects genes associated with superior milk production in cows. To develop this test, he poured over 38,000 key differences in cows on production records across the U.S. He then identified the genes associated with high milk production.

This provided Van Tessell and his lab at the USDA the information needed to determine which of the 38,000 genetic markers corresponded to animals that not only had the best genes for milk production but were actually passing these genes on to their offspring.

In the last century, pedigrees were only 30 percent accurate in identifying good dairy cows prior to their first lactation. And no pedigree had been better than 50 percent accurate in assessing whether either parent will pass on a particular trait. Now, with the aid of Van Tessell’s SNP test, accuracy has shot up to more than 70 percent.

Up to this point, commercial bull studs have played a major role – unseen by most of the public – in advancing the dairy industry. Artificial insemination of cows is now the norm on many dairy farms and first became commercially viable in the 1940s with the help of dry ice. When liquid nitrogen storage equipment became available, the business really took off.

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And in the past 30 years alone, the practice of artificial insemination has resulted in genetic improvement that can be attributed to an 80 percent increase in milk production in Holstein cows.

Bull stud services selected genetically superior bulls to be put on progeny performance evaluation. These companies collected semen from each of the young bulls they purchased or leased. The semen was put in liquid nitrogen storage and used in selected herds across the U.S.

The resulting heifer calves were tracked through their juvenile stages until they became pregnant and calved. Their milk production was tracked through the 10-month lactation and compared to unrelated herdmates and herds across the U.S.

Generally, a bull was not considered of superior genetic merit until it had 20 daughters performing well in more than 20 herds across the U.S. This process – determining which bulls made the cut to graduate to the “executive suite” at the bull farm – took about five years. Only one in 20 bulls made the grade.

I estimate that today across the country about 500 bulls’ frozen semen is used to inseminate about six million dairy cows. (One healthy bull can produce about 350 to 500 doses of semen a week.)

Now, Van Tessell’s work is ready to take the dairy industry to the next level. The best feature of his work is that his SNP test – as little as $50 – replaces older tests that cost more than $50,000 each to detect the genes that support superior milk production. The concept of Van Tessell’s test is also being applied to other areas of animal agriculture.

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American dairymen have been very innovative in feeding and managing cows to increase milk production by about 2.5 percent a year. It is calculated that genetic advances made possible with this test will double that annual increase to 5 percent.

Van Tessell and his team are still hard at it. They are currently working on identifying the heritability of resistance to internal parasites. This would be a huge advance in the sheep and goat world.

Another project on the drawing board is identifying the genes that give a cow resistance to bovine respiratory disease complex. Recently, Van Tessell’s team was awarded a $2.98 million grant to work with five major universities to identify other economically useful genes that promote food animal production.

Feed efficiency, only detected as a moderately hereditable trait, is of particular interest to me, as it surely is to dairymen. Some cows are genetically capable of maximizing milk production from the feed consumed. Dairymen with those cows are able to “milk” more income while minimizing feed costs.

Chuck Sattler of Select Sires says cows with this trait currently demonstrate an advantage in profitability of $0.24 to $0.26 per cow per day. And there are a host of other, lower heritable traits that also can be evaluated through the SNP test.

Bull stud operations have quickly adopted SNP technology because it cuts substantial expense and guesstimating from selecting bulls for their genetic merit. While it hasn’t reduced the age of the bulls entering the stud, it has reduced the age of the parents of these bulls selected.

Formerly, a bull’s dam had at least one lactation prior to the bull entering a stud. Now, a bull is born from a heifer and genomic young sire, effectively reducing the generational age from five years to 2.5 years – a 50 percent drop.

According to Dr. Kent Weigel, chairman of the department of dairy science at the University of Wisconsin, you can effectively use genomics in a commercial herd. Here are his thoughts:

  • Genotyping is most informative for animals with missing or incorrect ancestry information and that don’t have phenotypic data of their own.
  • Whole-herd genotyping can be cost-effective if pedigree and performance data are limited.
  • Pre-sorting animals and testing a subset that is at risk for selection or culling may be beneficial.
  • The genetic gain needed to offset testing costs is strongly affected by the number of animals retained.

Most SNP genomic testing chips on the market are 50K or 80K SNP chips, capable of testing 50,000 or 80,000 alleles – the DNA codings of a gene that determines heritable traits. The cost to evaluate a bull using either the 50K or 80K chip runs $125 to $150.

There is a 9K SNP chip available that most dairymen use. It costs about $45 to $50 per test. Even though it provides less powerful information, the 9K chip is adequate for dairymen testing heifer replacements.

A 780K chip was recently introduced, but it so far hasn’t provided additional information to improve milk production efficiency. Hopefully, they will soon have its benefits sorted out.

Zoetis has developed a genomics test which is designed to identify several desirable traits. Merial also has a genomics test geared more for beef cattle.

Here is an example of an effective method for using genomics in a commercial herd:

  1. Submit testing cards with hair or blood samples to a lab when each heifer is 4 to 5 months old rather than waiting until breeding age. This provides an opportunity to reduce feed costs by removing low genomic heifers earlier.
  2. If the test determines that genomic predicted transmitting ability (GPTA) for lifetime net merit is more than $600, flush once and then breed to the best available A.I. bull based on recommended pedigree mating.
  3. If GPTA for lifetime net merit is $400 to $600, breed to the best available A.I. bull using sexed semen.
  4. If GPTA for lifetime net merit is $200 to $400, breed to the best available A.I. bull using conventional semen.
  5. If GPTA for lifetime net merit is $75 to $200, use as a recipient for a fresh embryo or frozen embryo (if fresh is unavailable), or breed to an A.I. bull in the 80th percentile (if fresh and frozen embryos are unavailable).
  6. If GPTA for lifetime net merit is less than $75, breed to an A.I. bull in the 80th percentile and sell as a short-bred heifer.

Another option that has become more apparent in the past few months is to breed these low genomic merit heifers to beef bulls. Because of the marked decline in the national beef herd, some beef cow-calf operators are paying a premium to purchase crossbred heifer calves to increase their herd size.

One thing is for certain about today’s genetic selection: There’s no going back to the day depicted in the calendar photo where the dairyman got caught in a rainstorm leading his one and only cow down the road for service by the neighbor’s bull. PD

  • Donald Sanders

  • Associate Professor
  • Ohio State Universtiy

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