Genome Sequencing’s Impact on Selection Decisions
by Kasey Brown, associate editor
BILOXI, Miss. (June 10, 2015) — In the last 15 years, the cost of sequencing 1 million base pairs has dropped from more than $5,000 to 5¢, said Jared Decker. The assistant professor and beef genetics specialist at the University of Missouri spoke during the technical breakout session on advancements in selection decisions at the 2015 Beef Improvement Federation (BIF) Annual Convention in Biloxi, Miss., June 9-12.
Jared Decker highlighted opportunities with genome sequencing now available due to leaps in technology.
That intense price drop illustrates the journey of genomic sequencing, and opportunities abound. Genomic sequencing has hit some rocky patches since the 1970s. The available technology wasn’t always up to par, or assumptions didn’t always reflect the data or biology, Decker explained. In 2009, the bovine reference genome sequence assembly was published, genomic predictions were implemented in the dairy industry and the entire DNA was taken into account. Angus Genetics Inc. (AGI) implemented genomic predictions in 2010, followed by several other breeds in 2012.
With the great leaps in technology, Decker highlighted some options of future opportunity with genome sequencing. Imputation is on the near horizon. He gave the example of mile markers vs. points of interest on a road trip. With enough background data, those “mile markers” could be predicted from the data at those “points of interest.” He said scientists can infer 11 million markers from a 50,000-SNP chip. A finer scale and more precise analysis allows scientists to identify SNP regions associated with a specific trait.
Decker predicted more types of SNP chips or panels, including higher-density panels focusing on functional variants for research, and lower-density panels focusing on functional variants for prediction. Additionally, he added that genomic predictions would be based on causal variants or closely linked variants, which could lead to lower cost and more precise predictions.
He mentioned genomic “surveillance” of influential sires. Breed associations could sequence a sire when he reaches a certain number of progeny equivalents, which would mean progeny, grand progeny and farther down. This could lead to early identification of possible functional variants, both good and bad — like embryonic lethals. This could also help manage inbreeding based on shared negative variants.
Decker explained that genomic sequencing is in the upward trend deemed the “slope of enlightenment,” and he concluded that there are many possibilities.
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 of the tour stops.
Editor’s Note: This summary was written under contract or by staff of the Angus Journal®. Through an agreement with the Beef Improvement Federation, we are encouraging reprinting of the articles to those who will adhere to the reprint guidelines available on this site. Please review those guidelines or contact Shauna Rose Hermel, editor, at 816-383-5270. PowerPoints are posted with permission of the presenter and may not be reproduced in whole or in part without the express permission of the presenter.
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