Genomic technologies may soon be available to predict traits in commercial cattle, according to University of Alberta researchers.
Graham Plastow, CEO of the University of Alberta’s Livestock Gentec Centre, spoke about current opportunities for commercial producers to benefit from genomic tools and technologies in development during the Canadian Beef Breeds Council’s Technical Forum. This was held in conjunction with the 2018 Canadian Beef Industry Conference in August in London, Ont.
The Livestock Gentec Centre is currently developing genomic technologies geared towards crossbred cattle. Researchers studying genomics examine the structure, function and evolution of DNA and genomes. Many genomic tests use Single Nucleotide Polymorphism (SNP) technology to identify variations in a DNA sequence, which provides the unique genetic makeup of an animal.
Breed associations and other partners are already using this technology to increase the accuracy of Expected Progeny Differences (EPDs), which are predictions of an animal’s genetic value in producing progeny. Genomically enhanced EPDs are more reliable for selecting young animals with no offspring, providing a more accurate prediction of their progeny’s traits.
The development of genomically enhanced EPDs for crossbred cattle could be used to better predict an animal’s value, whether it’s a bull’s ability to sire productive daughters or a steer’s carcass traits. Plastow gave an example of comparing the performance of two steers that were almost identical in physical appearance.
“The more efficient steer gained the same weight in the lot as the inefficient steer, but it ate nearly 500 pounds less,” he said. “We couldn’t see that, but if we generate the genomics tools to predict it, think of the value that would have.”
To outline the potential value of hybrid vigour, Plastow referenced a paper recently published in the Canadian Journal of Animal Science, authored by John Basarab, senior beef research scientist at Livestock Gentec, and other researchers. The study looked at breed composition and retained heterozygosity, or hybrid vigour, in 412 replacement females over five calvings. Researchers found that each 10 per cent change in hybrid vigour resulted in positive outcomes such as higher pregnancy rates, weaning weights, lifetime productivity and longer survival in the herd.
“These differences resulted in an extra $161 per heifer per year,” said Plastow.
Commercial producers could use this technology to better select for increased productivity, fertility and longevity. While studies show that crossbreeding can increase these traits by 20 to 30 per cent, Plastow reported that the number of offspring in the Canadian calf crop has been steady for about 30 years at 83 to 85 per cent.
“That’s remarkable because we’ve improved a lot of things in the industry — management, nutrition — but we’re still down at this level,” he said. Since the early 2000s, there has also been a decline in hybrid vigour resulting from single breed use. “It’s very quick to be able to lose track of the level of heterosis in the herd.”
The decline in hybrid vigour is a short-term opportunity for researchers, Plastow later explained, allowing them to work on it while developing the technology for their long-term goal.
“We realized this was an issue we could tackle with the data we had already collected, as it relates to the level of crossbreeding which can be estimated directly by using the genotype,” he said. “We have so much detailed information on the breeds, we can determine the level of heterosis in a cow herd using a relatively small number of SNPs, compared to predicting accurate EPDs for crossbred cattle.”
Structure of the beef industry poses challenges, opportunities
Genomics played a major role in adding value to the Canadian dairy industry throughout the past decade.
“I think the dairy industry… was perfectly set up to use genomics,” said Plastow. The predominance of the Holstein breed and the bull test system helped ease the dairy industry’s adoption of genomic technology.
Before genomic technology was introduced in 2009, the net annual value of genetic improvement to the dairy industry was $265 million per year. After the introduction of genomics, the net annual value of genetic improvement to the industry between 2009 and 2014 had increased to $540 million. It is predicted that this value for 2015 to 2019 will rise to $748 million per year.
However, using genomics to create similar value is more difficult for the Canadian beef industry, due in part to the variety of breeds used.
“That’s one of the reasons why it’s been tricky to take this technology forward, particularly for the commercial producer. We use a lot of crossbreeding and we use natural service, and because we have some other elements the problem becomes even more complicated,” said Plastow. Other research challenges include the fragmentation of the beef value chain and the variety of management systems and environments across Canada.
Plastow believes that despite these challenges, the Canadian beef industry is in an ideal position to benefit from genomics, especially with commercial herds. One application already available through breed associations is SNP tests used to identify parentage. For example, Delta Genomics offers a product called EnVigour HX, which uses hair samples to provide producers with an analysis that includes genomic breed composition, parentage verification and a hybrid vigour score.
“Parentage assignment does have value in the industry, particularly in choosing the best animals to go forward, choosing replacements. That’s something that’s very easy to do.”
The genomic research that has already been conducted allows for simple application of this technology. “With all of the data that we’ve generated through our genomics projects, funded initially by Genome Canada and carried on by Genome Alberta and other supporters, we have a fantastic database of cattle genomes, and we can use that to analyze samples from a cow herd, anybody’s cow herd, and determine the breed composition of the calves,” he said. “From breed composition we can determine the heterozygosity that’s in the herd, but importantly, in individual calves.”
Genomics can also be used to evaluate a bull’s performance. Plastow provided an example of a study charting the progeny of 118 sires, illustrating that some bulls were producing at a higher rate than others. However, he noted that it’s important to know if the bulls that sire the most calves are also siring the best calves.
“Those two things are linked. You need to be selecting the best sires and you also need to know if they are doing the job.”
With SNP tests available for about $45 each, Plastow sees a decent return on investment, given the cost of retaining females and maintaining bulls, plus the potential added value to breeding programs.
“You can use these tools for better mating and culling decisions or selecting for replacements. We’re beginning to see more accurate genetic selection, and you can also use them to be part of branding plans.”
Other applications that are being developed at Livestock Gentec may add even greater value. “Ultimately, we want to be able to generate predictions of value indices for commercial cattle. That’s the bit we’re still struggling with.”
Support from Genome Alberta and Alberta Agriculture is helping to make these tools available to producers in the near future, and Livestock Gentec is focused on providing applicable information and technology.
“We’ve been thinking very hard about how we can use some of the knowledge we already have to help the industry,” said Plastow. “This is really where we’re trying to go, to improve the predictions for commercial cattle, but we’re not there yet.”
However, he reported that researchers have made progress in using genomics to better predict certain traits. “The project is looking at all the variants we have access to now to try and improve the efficiency of our predictions in the crossbred herd,” he said. “We’ve gone up from about 20 per cent and we’re between 30 and 40 per cent now by refining these tools.”
Measuring phenotypes will still be necessary. Plastow explained that genomic technology is most useful when examining traits that are difficult to measure and thus more expensive.
“If we’re going to identify who the best animals are or mate them, we have to measure the phenotype,” he said. If researchers can find links between SNPs and a trait, they can use genomics to make predictions, he added.
Other related opportunities may be available in the future. Feed efficiency is a priority for researchers at Livestock Gentec and Plastow anticipates that genomic technologies will soon be used to improve feed efficiency.
“We’ll still need to measure some of the animals for the trait to continually refine and maintain the accuracy of these tools, but we’ll be able to bring some of these new traits, like feed efficiency or tenderness, into scope.”