BRD Genomic Testing
DNA pooling offers alternative to discover genomic traits associated with bovine respiratory disease.
by Kasey Brown, associate editor
BILOXI, Miss. (June 10, 2015) — Researchers have a similar problem as cattlemen in that genetic testing is expensive. This makes economically important research, like that of determining genomic traits for bovine respiratory disease (BRD), difficult. Larry Kuehn, research geneticist with the USDA Agricultural Research Service and the U.S. Meat Animal Center (USMARC), explained an alternative — DNA pooling.
Kuehn said DNA pooling offers an alternative, though limitations must be taken into account.
Larry Kuehn shared research that is working to identify SNPs associated with severe lung lesions in fed beef cattle. The research team sampled 11,520 lungs from a Nebraska processing plant, and the majority of lungs came from cattle raised without antibiotics.
He shared research methodology at the technical breakout session on advancements in selection decisions during the Beef Improvement Federation (BIF) Annual Convention June 9-12 in Biloxi, Miss. The cost of testing 96 animals with a high-density test is $14,880, but testing a pool of 96 animals costs $155. The data need extra imputations when pooled, but it does present a significant cost savings.
Pooling DNA has opened up more research opportunities at USMARC, including studies on lung lesions, diseases like BRD, foot rot, pinkeye, bovine viral diarrhea, bloat, pregnancy detection and more.
He shared research that is working to identify SNPs associated with severe lung lesions in fed beef cattle. The research team sampled 11,520 lungs from a Nebraska processing plant, and the majority of lungs came from cattle raised without antibiotics.
He admitted that the research isn’t at a producer-application level for national cattle evaluation yet, but results are useful from a research perspective. Seven SNPs achieve genome-wide significance at the 5% level, and 84 SNPs achieved a false discovery rate of 5% or less. Near-significant SNPs were found for tissue repair and regenerations, tumor suppression, control of organ size and immunity.
“We reduced the cost of genotyping by exploiting sample pooling of extreme animals, and we identified SNPs that might be useful to reduce BRD complex and reliance on antibiotics,” Kuehn explained.
He highlighted a future study that will look at feedlot BRD, and said he hoped that the lung and feedlot project will produce complementary results to keep moving forward.
The 2015 BIF Annual Convention was hosted by Mississippi State University and the Mississippi Extension Service June 9-12 at the Beau Rivage Casino and Hotel in Biloxi. The Angus Journal and LiveAuctions.tv provide comprehensive online coverage of the event at www.BIFconference.com. Visit the Newsroom for summaries, proceedings, PowerPoints and audio of the sessions; the Awards page for announcements of award winners; and the Photos page for photo galleries the tour stops.
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