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Group vs. Individual Genomics

Geneticist discusses use of DNA pooling for validation of genomic predictions.

by Lindsay King, assistant editor, Angus Journal

LOVELAND, Colo., June 22, 2018 — Genomics can be a fairly affordable process, but if there were a way to make it even more cost-efficient, would you be interested? Larry Kuehn, a USDA-ARS research geneticist for the U.S. Meat Animal Research Center, introduced the idea of DNA pooling that could do just that.

“We are beginning to understand that we are doing things that are making genomic evaluation better,” Kuehn said. “We have all kinds of breeds out there using genomically enhanced EPDs (expected progeny differences). People are using these more consistently throughout the industry, and we are all better for it.”

Data is being collected at a rapid rate; however, there is still plenty more data seedstock producers need to collect. Genomic information is no small task to collect for an entire herd, and genotyping an individual animal can be expensive at times. Many producers also don’t want to simply give information to the industry for free since they invest quite a bit into it.

“We can use lower-cost methods to genotype groups rather than individual animals,” Kuehn explained. “DNA pooling combines samples from multiple animals to obtain a group genotype.”

Used frequently in research trials, DNA pooling looks for differences in gene frequencies between high and low groups for a marker to show if it is effective for a trait or not. The high and low groups refer to the top and bottom parts of a chromosome known as chromatids.

“Most breeds are using a single-step procedure with a relationship matrix based on genomic data in their national cattle evaluation (NCE),” Kuehn said. “Genomic relationships between animals with pooled DNA and individual genotypes can be derived in a similar fashion.”

The cheaper option, genotyping a group through DNA pooling, costs almost as much as individually evaluating less than five animals. This method could still detect sire contributions and reveal which bull was contributing the most to the progeny and the pool.

“DNA pooling would allow producers to get an idea of the genetic merit of individual animals through multiple bulls by finding sire contributions within several pools and averaging them,” Kuehn said. “This would be a great complement to commercial marketing programs and could further adjust prediction means using a tool like this across all-breed EPDs.”

Some challenges to adoption of DNA pooling derive from the high cost of tissue sampling. In addition, there is continued need for more research about variation in contribution to the pool.

“With a larger pool size there is less variation in contributions, but also less variation in group means,” Kuehn said. “We also need to make sure we are not over-representing a single animal. However, we are probably not too concerned about that because the pools have been big enough to combat that.”

One of the next steps toward adoption is getting commercial entities to collect tissue, record data and then release the group means and genotype pool. The value comes from capitalizing on genomic variation as well as breed.

“Breed composition and physical characteristics are usually the primary buying criteria for feedlot operations and often drive weaned calf prices,” Kuehn said. “DNA pooling could substantially improve basic visual appraisal through genomic validation.”

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