Genotyping adds up

Lower cost testing can give you a real advantage when it comes to advancing your herd's genetic progress more quickly

The cost of genotyping has dropped to the point where it is opening up possibilities for widespread testing by Canadian dairy producers. In September 2010, the launch of GenoTest, the national genotyping service, made this testing available through Holstein Canada for $47 per test using the 3K chip.

Even at this price, you could ask whether there are enough reasons to test your herd or even part of it. If you look at genomic testing of a newborn calf as investing in future useful information for managing and improving your herd, it can be well worth it.

Genomic testing of females at an early age identifies basic genetic information. You can add further information as cows create records in their own right.

As well as benefiting your own herd, more genomic testing of females broadens the scope and numbers of the national herd that have been genotyped. These increased numbers are necessary to update genomic evaluations and generally improve their accuracy.

The 3K test's most effective use is identifying the genomic estimated breeding values (EBVs) of female calves. The 3K chip increases parent average EBV reliability to the level you would expect only after a female achieved one or more records. This lets you apply some selection decisions, typically made in first lactation, at the newborn level.

The 3K chip offers reasonable accuracy at a much reduced cost if at least one of the parents, usually the artificial insemination (AI) sire, has been tested with the more expensive 50K chip. When parental information is available, the 3K chip provides almost as much accuracy, as shown in the table from Holstein USA on page 42.

Relative reliability is the same in Canada, and applies in much the same way to other traits. Some lower heritability traits actually benefit relatively more from the added information you get from genotyping.

Most AI bulls have been genotyped with the 50K chip. This helps impute a value for a female tested with the 3K chip when there is probably a genomic EBV for her sire as well as maternal grandsire.

Parent averages have limited usefulness for making selection decisions. When chromosomes split for reproduction, a sample half of the genetic material goes to form the sperm or egg.

Although two or more heifers may be full sisters, we did not know the exact mix of important chromosomes each would have inherited from their parents-until the advent of genomic testing. The reliability boost we get from using the 3K or 50K chip reflects that new knowledge we have gained from genome mapping, providing a much better estimate of the actual genetic makeup of that individual.

There are three billion pairs on 30 chromosomes in the bovine genome. Recently, an 800K SNP chip has been introduced that identifies 800,000 sites. Not enough is known about all the sites included on this chip to tell whether it will be of much greater value in identifying important dairy cattle traits.

Although the 3K test's 65 per cent reliability is far from perfect, you could use it effectively to work with groups of replacements. A l00-cow herd, for example, would have 40 heifer calves born per year. At $47 per animal (2010 price) for 40 3K tests, the cost would be $1,880, excluding your time. Genomic test results would be transmitted to the Canadian Dairy Network (CDN), and the genomic EBVs would be reported to you the same way you receive parent averages now. Current costs can be found on the Holstein Canada website (

In the absence of more complete economic modeling of breeding decisions based upon genomic information, here are a few possible scenarios where this information could benefit the dairy herd owner in making herd breeding decisions.

The improved accuracy of genomic EBVs would help rank all replacement animals more accurately as well as identify the extremes: high genetic merit and low genetic merit. This would more accurately predict which portion of your replacement herd will be profitable once they have calved. By gnomically testing all replacement females they can be ranked according to how productive they will be in first lactation and culling decisions made accordingly.

The lowest genomic EBV heifers are most likely well below average once they are in the milking herd, so removing the lowest ranking heifers would give you the quickest payback for genomic testing. Removing these heifers early in life instead of calving them out and culling early in first lactation means you would save the $2,500 per heifer cost of raising them, less the difference in salvage value-probably about $400 per animal. Benefits would vary, depending on relative value of replacements and cull cows.

Potentially up to 25 per cent of the heifers could be removed in this manner. Nevertheless, cost savings of culling as few as one or two heifer calves based on their genomic EBVs would recoup testing costs.

The remaining heifers that do enter the milking herd are going to be more productive due to the selection decisions made using the genomic information. This advantage would result in higher profit in every lactation as long as they remain in the milking herd.

Alternate strategies would be to breed the low-ranking heifers to beef sires or use them as ET recipients. You would still be calving them out, and cost savings would not be immediate since you would incur the cost of raising all replacements.

An alternate approach would be to select the top 10 to 20 per cent of heifers and breed them to sex-sorted semen to ensure female offspring. This strategy actually increases your investment, but ensures better quality heifers and more rapid herd improvement. It could involve testing only the top half of the replacement heifers according to their parent averages, lowering the cost of testing at the risk of missing a few high GEBV individuals.

A similar approach would identify the top 10 per cent of heifers as embryo transfer donor candidates, and the bottom 20 to 30 per cent as recipients. This is a costlier strategy but, again, would move your herd forward genetically much faster.

A herd marketing top breeding stock, possible bull mothers or embryo transfers, possibly for export, should take full advantage of genomic testing through the 50k chip test. These breeders should consider screening the remainder of their herds with the more economical 3K chip test.

However, if you raise all replacement females and calve them out because you need them all to maintain milking herd numbers or you prefer to cull heavily in first lactation genomic testing offers no benefit. You would not be taking advantage of the genomic information early in life when it is most effective, and not recover testing costs.

If you do decide to take advantage of this technology, you could enhance profitability through rapid herd genetic improvement, herd enlargement or reducing the cost of raising replacements by removing those calves with low genetic merit. Genetic improvement revolutionized.

This article first appeared in the Ruminations column of The Milk Producer Magazine in March 2011.

Table 1. Projected Reliability of 3K and other tests for milk in Holsteins
Source of genetic Genomic information Projected
prediction available reliability
Parent average None - tradional method
3k chip on animal Sire and MGS with 50K test,
  Dam not tested
3K chip on animal Both parents tested with 50K chip
50K chip on animal Imputation not needed
800K chip on animal Imputation not needed

For more information:
Toll Free: 1-877-424-1300
Author: Blair Murray - Dairy Genetic Improvement Specialist/OMAFRA
Creation Date: 02 December 2011
Last Reviewed: 10 February 2012