Genomic Evaluations:  the next advance in genetics technology ?

$54 million is being spent on research into mapping the bovine genome (DNA) and identifying the SNP “marker” genes that indicate the desired direction in genetic traits.    It is an internationally funded effort but the work is being performed by Agricultural Research Service [ARS-USDA: same bureau contains Animal Improvement Programs Laboratory (AIPL) that calculates sire summaries and cow indexes.]    

What is an “S N P” ?

Single Neucleotide Polymorphism.    In other words, a DNA structure possessed by a breeding animal  that is able to indicate directional change in a trait.     We call them “gene markers” in part because we know they are linked to specific identified traits, and that they show up at the same location on the DNA no matter which animal possesses them.

How did we find them ?

AIPL collected DNA samples on over 6100 animals [mostly bulls with extensive AI service], and compared their DNA structure to their genetic evaluations for all summarized traits.    Patterns in common were summarized, and eventually 70,000 “links” between the data set and the microscopic views have been verified from 5285 of the samples.     [This from approx two million bovine genes.]

How is this data being used?

Those organizations who agreed to help with funding and to collect and submit DNA samples will now receive “Genome enhanced” PTA value assignments for their new young sires.    Whereas the traditional “Parent Average” estimation of a YSP sampling sire’s “genetic value” only had 35%-40% “Reliability” [relative data accuracy], the genome-enhanced PTA values assigned are being given 70% Reliability.

On individual data I have seen, the most frequent use of this procedure is to screen among ET full sibs to determine which calf has the “best” Genome profile, as an aid to increasing efficiency in sire sampling. 

Now, no matter how “good” the pedigree, if the Genome markers are absent, the bull will be passed by.

Among sire systems we represent, Taurus Service (stud code 76) is an active participant.   The first sires resulting from this enhancement will show up in 2009 young sire listings.

Does this mean we will see more/faster genetic progress ?

Only in YSP herds, as the percentage of “dud” bulls sampled on the basis of pedigree will decrease.    On the last data I saw, printed in Hoard’s Dairyman in an article by Dr Bennett Cassell, the average of ten years’ sire usage in DHI tested herds, showed “proven” sires at $121 LNM advantage, vs “sampling” sires at $86 LNM advantage, over cows milked sired by herd bulls.    The difference between “proven” and “sampling” sire usage across the population should decrease from this enhancement.

But whether rates of “genetic progress” accelerate, depends on whether sire analysts get better at picking matings to make, prior to the $400 DNA testing that can “enhance” their PTA estimates.     Based on a comparison of Bennett Cassell’s [H/D article] data to the sort of data released decades prior, it requires an increase in lifetime length (dependent on improving genetic rates of fertility) before we would see an acceleration of genetic progress, measured by “lifetime Net Merit.”    Short herdlife is the chief limiting factor in achieving genetic progress—not higher lactation yield volumes or heifer type scores.

Will Genomic Evaluations change the breeding industry ?

First—it raises the “up front” cost, in hopes of lowering the sampling costs (which are considerable, given only one in fifteen sires AI sampled ends up “active” on an AI marketing list).    So it could be a “barrier to entry” for startup companies or private sire syndicates, ie, an added 35% Rel up front costs a $400 DNA fee.     [note:  initial participants received a five- year advance usage for helping with their research, prior to allowing any competing firms to purchase test results from AIPL.]    But it has great potential to lower sampling costs for those who comprise AI’s “establishment” bull studs.

Note that the USA is not “first” with applying this technology:   LIC [New Zealand, stud code 190] is already utilizing the results of their ongoing genome research in their YSP sampling, and were some of the key consultants in designing the AIPL research effort.    [LIC sires are available in the USA through Taurus]

Our impression is that there may be no real impact at the dairy farm level, for these reasons:

(1)   It is focused to-date on “quantitative” gene effects.     Markers identified to-date tend to be linked to the traits used in genetic evaluation—production, type and “fitness” traits.    These sorts of genes are ones that are bi-directional and accumulate from selection [not all genes act in that fashion]. The data we use for sire selection will continue to be in the form of PTAs, and all traits not summarized will continue to have to be “guesstimated” from pedigree analysis and word of mouth. 

In fact, the very existence of genome data enhancement may impede the development of newer traits as demanded by dairymen—because each new trait will require an eventual reexamination of all those data sets, to determine if markers exist for each new trait.

(2)       Major areas of the genotype actually relate more to “Qualitative” and “Interactive” gene effects.

Qualitative genes are heritable effects that lack definite scales of measurement (non-linear, non-volume) and are more dependent on the mating selection than direct sire selection—ie, produce results not able to be predicted from a simple “averaging” of parent traits.    [These “qualities” form the basis of the “aAa” breeding guide, which does not use linear traits, recognizing these key differences.]

Qualitative gene action determines the individual physique as interconnected systems, and has a greater impact on the animal’s ability to adapt to environmental change than do quantitative genes.

Interactive genes represent the broad number of genes that only become “active” as a result of specific environmental “triggers”.    For example, relative to forage choices, whether the animal will gain weight or produce more milk (rumen efficiency)— whether the animal’s respiratory capacity can deal with high altitude (low oxygen density) air—whether the animal’s reproductive or immune systems continue to function above certain persistent levels of temperature and humidity.

(3)       The system tends to favor a continued narrowing of the breeding population.

How do you calculate the Genomic value of an animal bloodline that was discarded from the evaluation population (under prior, obsolete definitions of “genetic value”)?    Marker genes do not wear name tags you can read under the microscope.    While this may be an esoteric question (who cares about discarded genes?) the truth is, we have lost significant gene variety through the eras when (a) we did not “value” genetic fertility, (b) we did not “value” higher fat% cattle, (c) we did not value “body capacity”, (d) we did not value “strength” the same way we do today.    Changing times requires different mixes of genes.