Genomic testing on its way for bison sector

An Alberta firm says it will provide parentage verification, sub-species composition and the presence of cattle genetics

Edmonton-based Delta Genomics is moving closer to developing genomic testing tools for the Canadian bison industry.

Chief executive officer Michelle Miller told the 2018 Canadian Bison Association annual convention that the first two steps of a five-step process are complete, and over the next year the tools should be completed.

In the end, she said the company intends to be able to provide parentage verification and a full package test that includes parentage, sub species composition and whether cattle genetics are present.

The project began with the whole genome sequencing of 27 animals, looking at all three billion base pairs in the DNA.

Researchers used five Wood bison samples collected before 1925, including two from the Smithsonian Museum and three from the Canadian Museum of Nature.

“1925 was our cut-off year because that was the year that Parks Canada introduced Plains bison into Wood Buffalo National Park,” Miller said.

Plains bison had been compromised through crossbreeding with cattle.

Three Wood samples from 2018 in Elk Island National Park, eight pre-1925 Plains samples from the Canadian Museum of Nature and 10 more recent Plains samples from various geographical regions were also used. Miller said that included samples where they knew which year cattle had been bred into those herds.

The 27th sample was a “freebie” when a project called CanSeq150 decided to sequence 150 of Canada’s most iconic species in honour of the country’s birthday and included a Wood bison from Elk Island. Wood bison are considered a species of special concern.

Miller said the raw data from the 27 animals was shared with Dr. James Derr at Texas A and M University, who has worked extensively on bison genetics. In return, the Canadians received 14 whole genome Plains sequences and 50,000 SNPs, the commonly used term for single-nucleotide polymorphisms. These are variations in DNA that can act as markers.

The third step is now underway, and involves using the data from the Canadian and American samples to select the SNPs and develop three lists: parentage verification, Wood versus Plains composition, and cattle introgression.

For parentage verification, only a few hundred SNPs are required. The composition test will require about 7,000.

For the cattle introgression, Miller said they don’t know how many they will need.

“We’re trailblazing a bit on this one,” she said.

After the lists are developed, the researchers will validate the genotypes.

“We’re going to create a single test using all those SNPs from all three lists and then we’re going to run 480 bison on this test where we already know the answer,” said Miller.

Finally, once validation is completed, the tools will be launched.

Miller said the parentage verification test will probably cost producers about $25 and be available by the end of 2019.

The second test offering the full complement should be ready by the second quarter of 2020. The cost is still undetermined, but Miller said a similar test in the cattle industry was about $250 to start with and is now down to about $60.

Stewart Staudinger from MFL Ranches at Alix, Alta., has been testing his Plains bison herd at the University of California at Davis since 2013 with a goal of eliminating cattle genes.

His interest is to build on genetic purity and conservation to add value to ranchers’ bottom lines.

His entire herd was tested in 2014. Of the 130 cows and heifers, 23 were found to have bovine nuclear DNA and one had bovine mitochondrial DNA. Of nine bulls, three had the bovine nuclear DNA.

Staudinger said many herds won’t have as much mitochondrial DNA because it negatively affects performance; many producers would have naturally been selecting for it and eliminating animals that carried the DNA.

To eliminate the cattle genes, in 2015 the ranch carried forward 7.6 percent of the stock that had cattle DNA, including one bull.

Over the next couple of years testing and culling continued.

MFL shipped its last bull with bovine DNA in 2016 and its last cows in 2017.

“The 2018 calf crop for us is the first from a completely pure breeding herd,” he said.

Staudinger said Woods are considered pure, but producers who crossed their Woods with Plains may have introduced cattle genes into their herds.

He said there is a market for pure breeding stock and there is a strong interest in conservation in developing pure herds.

Parks Canada herds have been closed to new genetics, and that wouldn’t have been a natural state in the wild, he said.

Ranchers are the ones developing the pure genetics, and genomic tools will provide new management strategies for both Parks Canada and producers, he said.

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