Genomics—A scientific yet practical approach

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Published on: September 23, 2015

by Dr. Pat Comyn

Let us imagine that we are embarking on a journey across the Atlantic ocean in a ship. We have two different ships that we will compare. One ship is the USS Pregen, and the other the USS Genomic. Both ships are identical in speed and power. However, the navigation systems are quite a bit different. The Pregen uses traditional, time-honored methods to navigate. Theoretically, if USS Pregen left New York harbor a thousand times for the Thames river mouth, it would find the west coast of Europe within 700 miles of the Thames 50% of the time and find the western coast of Europe and North Africa 90% of the time. The USS Genomic, also leaving New York harbor a thousand times for the Thames river mouth, can get within 50 miles of the mouth of the Thames river 70% of the time and within 100 miles 95% of the time because of the use of more modern navigational devices. Both ships are crossing the sea at the same speed, but one with more accurate (but not perfect) navigation.

In brief, genomic evaluation compares the single nucleotide polymorphism (SNP) at every 40 to 45 thousand or so down to every 450 or so continuous pairings of nucleotides. Holstein genomic tests can be at lower density (meaning fewer SNPs assessed) of 9 to 12,000 (9 to 12k), mid density (78,000), or high density >700,000 SNPs (Dechow; higher density testing does not enhance reliability appreciably). The data from the SNP assay are then compared against other similar pedigrees where sire, and possibly dam and grand sires, have both genomic and phenotypic proofs of offspring from both DHI and breed association type scoring. I say possibly the dam. The female side of the pedigree generally does not bring a lot of information into the genomic picture because a dam is limited in how many offspring she can put into production. At the end of the day, genomic evaluation in Holsteins will in effect add 15 to 50 daughters to the proof reliability of a bull or heifer depending on trait. This will raise the reliability from say 35% to 70%. Lifetime net merit ($NM) calculations add the equivalent of 42 daughters (Dechow) in Holsteins. The less numerous dairy breeds such as Brown Swiss, Milking Shorthorn, Guernsey, etc. have a more difficult time with genomic testing. There has to be a population of contemporaries large enough to allow comparison. Without a contemporary population of sufficient size, reliabilities will not be high enough to really change breeding strategies from those used in the pre-genomic era.

The milk yield traits and type traits are proven pretty fast once daughters begin entering milk yield data. These traits tended to be among the most accurate going from prediction to proof pre-genomic as well. However, other traits such as productive life, fecundity indices, and feed efficiency, to name a few, require a different level of analysis in that they tend to have lower levels of heritability and thus need a lot more observations in order to find where an individual lies in a given population.

Animal genetic analysis is conducted in many countries on similar or seemingly similar breeds. Then data in these countries are worked into formulae that try to predict economic performance based on market trends in that country. So the United States has a TPI and NM, Canada has the LPI, and Germany has the RZG. All of these indices are based on data from animals in that given country and economic realities in that country. One has to understand that the average sire stacks in Germany or Canada will be quite different from those in the United States.

Since we as ET practitioners often work with embryo export, there are some things to be aware of regarding Europe and Genomics. First off, US animals that have a high gTPI tend to be high in, say, the RZG, but there is little relationship with actual ranking comparing United States to, say, the RZG. For instance, I had a Yoder ´ Day that was turned down by a US bull stud due to the gTPI being too low for the US market (@2420). He tested over 160 on the RZG (>155 to 158 RZG is interesting to German and Dutch bull studs, though they look more at individual trait indices than here in the United States). So a Dutch stud purchased him. One has to get a bull or heifer nominated by a bull stud in order to genomic testing in most European systems. This is something an ET practitioner can assist with: helping arrange to get an animal tested in Europe. The genomic data can be electronically transferred from Holstein USA (or from a bull stud if they paid for testing on a rejected bull). Don’t take no for an answer on the first rejection of a bull, especially if he is carrying over, say, 48 pounds of protein. The European market likes milk production and protein. Health traits seem to be of lesser importance. Type traits push foot/leg and udder heavily.

Some other traits that Europe and Canada evaluate more than the United States are temperament and milking speed. Temperament and milking speed are traits with a range of suggested heritabilities, from, say, 5% to maybe 20%. This is about in line with daughter pregnancy rate assessments used in the US $NM and TPI system. Udder traits will have heritability in the 20% range, whereas stature and spring of rib might be in the 40 to 50% heritability range. So genetic improvement is certainly feasible. The reason temperament and milking speed are not factored in the United States is that they are not incorporated into the NM or TPI formulae. If they were, emphasis would begin to be placed on these factors from a breeding perspective. Temperament extremes do tend to weed out of a population, but taking a more scientific approach might save on workman’s compensation plans on farms over time. Similarly, selection for more rapid milk out could be attractive to producers pushed on parlor size versus number of cows to be milked.

I would like to thank Dr. Chad Dechow at Pennsylvania State University for his assistance on this article.

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