Genomic Prediction
Turning DNA Testing Into a Powerful Selection Tool
by Chuck Sattler, vice president - genetic programs
New research from USDA shows that DNA-chip technology can be used to dramatically improve the accuracy of genetic ranking son young animals. Initial results indicate the new methods nearly double the accuracy of traditional genetic evaluations on young animals. The reliability levels for the genomic predictions on young animals are improved but still somewhat less than the levels we see in first-crop progeny-tested A.I. sires.
World-Class Research
The results of the USDA research were first presented in January 2008. It was the first publication of successfully applying high throughput DNA testing technology to improve selection accuracy. This hasn’t been done before in any other livestock species or anywhere else in the world. This research effort was led by USDA and included contributions from several universities and industry partners.
This new approach is a direct result of the international effort to sequence the cattle genome completed just a year or two ago. It also takes advantage of new laboratory equipment that allows testing for 50,000 genetic markers at once. Previous marker assisted selection efforts used, at most, several dozen genetic markers.
The USDA effort involved assembling DNA from 5,360 proven A.I. sires, DNA testing each of them for 54,000 genetic markers and then doing statistical analysis to estimate the impact of each marker on a variety of traits. The analysis results from these historical animals were then combined with traditional pedigree and performance data to provide a genomic prediction. By using a large number of markers, the system accurately tracks the inheritance of each segment of chromosome from generation to generation and more accurately defines the pedigree makeup of
each individual. Genomic predictions then summarize whether the inherited DNA is favorable or unfavorable for traits of interest.
Improved Accuracy
The old adage of "mate the best to the best and hope for the best" has been carried out by A.I. programs for years. The competition level is high and in the end, what separates the breed greats from the others is whether or not they inherit an exceptionally good set of genes from their parents. With our current program we don’t know which bulls got lucky until they complete progeny testing. With genomic prediction, we will get an early and comprehensive indication of which bulls received a favorable assortment of genes from their superior parents.
Genomic predictions build upon our traditional evaluation system and add to it information about what DNA the animal inherited from its parents and grandparents. Incorporating this additional information makes the evaluation more accurate.
To document this accuracy, USDA went back in time and took their database as it existed five years ago and ran the genomic predictions. This was a test to see if we had had this technology five years ago, how well would we have predicted today’s evaluations for these animals? Table 1
summarizes the results. It shows that, for all traits, genomic predictions were considerably more
accurate than with pedigree information alone. In some cases, genomic predictions more than doubled the accuracy. The values presented are the realized accuracy of the Parent Average (PA) or genomic predictions. These values are a little different than the genetic evaluation reliabilities that are routinely published.
Another key point from this table is that genomic predictions fall short of the accuracy achieved through progeny testing. Genomic predictions will be helpful in making our progeny testing programs more efficient. With the current state of technology, however, it doesn’t appear that they
will replace progeny testing. Progeny testing will need to continue to provide the accuracy we’ve become accustomed to seeing in our A.I. sires.
Select Sires Leads the Way
Select Sires has worked hard over the past several years to incorporate DNA technology in our breeding program. Because of this effort, Select was poised to quickly take action when genomic predictions became available.
Beginning in February 2008, Select Sires began testing bull calves and using USDA’s genomic predictions to decide which ones should enter the Program for Genetic Advancement (PGA). By the summer of 2008 all Holsteins entering PGA will have genomic predictions and the ones with unfavorable results will be removed from the program.
Table 2 is an example of genomic predictions we received on a group of bull calves resulting from a contract mating for Select Sires. Previously, this group of full brothers would have been considered genetically equal. With genomic testing we were able to get an indication of possible
genetic differences between these calves. While these genetic predictions aren’t 100 percent accurate, we chose calf No. 4 because it appears he has received the best combination of production, type and fitness genes. Genomic predictions are in the early stages of development
and improvements can be expected as our database of tested animals expands and as the methodology improves. USDA is currently developing systems to routinely provide genomic predictions for the industry. Work is underway to incorporate genomic predictions into official genetic evaluations for January 2009.
Even in these early stages, though, it appears genomic predictions can be useful in helping make more accurate selection decisions on heifers and cows as well as for bulls going into progeny-testing programs. Genomic predictions will provide a noticeable boost to the rate of genetic progress by raising the accuracy of our selection decisions, improving the graduation rate of our PGA system, as well as reducing the generation interval of the overall breeding program.
Through our federated structure and wise investments in technology by your cooperative’s
leadership, Select Sires is poised to take advantage of this new technology to deliver industry-leading genetics to you through a highly selected group of A.I. sires.
TMProgram for Genetic Advancement and PGA are trademarks of Select Sires Inc.
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