Genomic Testing Pays

November 28, 2011 12:18 PM
Genomic Testing Pays

Can be used for culling bottom end

Commercial dairy producers might think that genomic testing of dairy heifers is only for registered breeders who make a supplemental living selling breeding stock.

Think again, says Tom Lawlor, a geneticist with the Holstein Association USA. Rapidly decreasing genomic testing costs open up a new array of strategies not only for finding elite animals, but for identifying bottom-of-the-herd culling candidates as well.

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More on genomic culling

The 3K chips, usually priced at $45 or less, have a Reliability of 60% if a sire has been genomically identified. That jumps to 65% when the maternal grandsire has also been genomically identified.

Genomic testing works particularly well for producers who have excess heifers and want to cull or sell low-end genetic potential animals. If those extra heifers aren’t needed to maintain herd size or fuel expansion, savings in feed and labor can be significant by not raising them to freshening.

Lawlor cites the example of a producer who tested 46 heifers with no sire or dam identification. The range in Net Merit dollars (NM$) was –$600 to +$600. The heifers were tested with a 3K chip, which cost about $43 per test.

By culling the bottom 10%, most of which showed NM$ of less than –$500, the producer raised the average NM$ of the remaining 41 heifers by $52.50, for an increased income of $2,153. The cost of testing all 46 animals was $1,978, leaving a profit of $175. And that doesn’t account for feed, labor and other costs saved by not raising those extra five heifers. Those could tack on $5,000 to $7,500 in savings.

If the producer had culled the bottom 10 animals from the group, he would have been able to raise his NM$ average by $92 on the remaining 36 animals, for an income of $3,312. Subtracting the testing cost of $1,978 would leave a profit of $1,334. And again, savings of not raising the culled animals would be substantial.

If the sire of the heifer has been genotyped, the genomic test will identify him. In commercial herds with no pedigree data available, the sire is identified about 50% of the time, improving Reliability. With that information, culling the bottom 10% would increase profitability to nearly $1,000.   

If a producer has both sire and dam identification, the resulting parent average will allow the animals to be ranked. With genomic testing, the producer would need to test only the bottom 50% of the group to identify the lowest-ranking animals. In other words, he can cut his testing cost in half while having even more assurance that he is making the right decision. That’s because the Reliability of sire ID is 30% for a trait such as milk production, 35% for sire and dam ID and 60% for sire, dam and genomic testing.

Even if you don’t genomically test your heifers, Lawlor says, you can benefit by buying semen from bulls that have been genomically screened. All young sires coming into AI bull studs are now tested.

But don’t go whole hog on any one bull. "Manage your risks better when selecting young sires by using a small quantity [of semen] from a wide variety of bulls," Lawlor says. 

Genomics Might Slow Inbreeding

The conventional fear about the heavy use of genomic testing is that it could speed up inbreeding, already at dangerous levels in Jerseys and rapidly approaching levels of concern in Holsteins.

The reason: If AI firms and purebred breeders can more easily identify top genetics through genomic testing, they could intensively select these animals and overuse them as the sires of sons and dams of sons.

But analysis by USDA’s Animal Improvement Programs Laboratory (USDA–AIPL) suggests genomic testing might actually slow inbreeding. That’s because genomic testing typically allows breeders to identify the superior animal out of an embryo flush of sons.

That individual is then selected by an AI stud to be brought in as a potential sire. His brothers are not brought in for AI service, and are most likely sold for beef or limited natural service.

But genomics has a downside as well. Because genomic testing is more accurate, AI firms are bringing more young sires into wider service and distribution much earlier—about as soon as they can produce semen.

The AI firms no longer go through an extended progeny test on young sires, waiting four or five years for those results before offering semen from the young sire for widespread use. This substantially shortens the generation interval. 

"Even with lower inbreeding per generation, the faster generation interval can cause the inbreeding rate per decade to increase," says Paul VanRaden, a dairy geneticist and one of the authors of the USDA–AIPL study.

"Also, estimates of merit are more accurate for chromosomes that are more popular, which makes finding good outcross genes more difficult," he says.

There is some good news, though. As genomic testing becomes cheaper and more widespread, particularly on heifer calves, producers will be able to incorporate that information into future
breeding decisions. "Using genomic instead of pedigree relationships [in mating programs] is a more precise way to avoid inbreeding," VanRaden says.

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