As anyone prepping kids for the first day of school can attest, things don’t always go the way you planned them. The same cannot be said for the Genome Alberta project to develop more accurate genomically-enhanced breeding values for traits of importance to the commercial cattle industry. With the project winding down, those behind it are upbeat about the progress to date. Part 1 of this two-part article looks at how the study began and what it sought to accomplish. Next month, Part 2 will explore the outcomes and the intriguing potential for industry.
“This project was put together in 2014 as part of the Genome Canada large-scale applied research program application,” said Dr. John Basarab, adjunct professor at the University of Alberta and Senior Beef Research Scientist at Alberta Agriculture & Forestry. “The proposal went through a ‘Dragon’s Den’ type of review in Toronto and got down to the final stage, but wasn’t selected. Fortunately, Genome Alberta felt the project had merit that warranted partial funding for four years.”
While funding is critical for any research, having the right players in place is equally vital. In addition to Dr. Basarab, co-leads on the project included Dr. John Crowley - research geneticist with the Canadian Beef Breeds Council and Livestock Gentec at the University of Alberta – and Dr. Donagh Berry, a quantitative geneticist based at the Animal and Grassland Research and Innovation Centre in Ireland.
Other major contributors to the project included Dr. Graham Plastow - CEO of the Livestock Gentec Centre at the University of Alberta; Dr. Paul Stothard, associate professor - Bioinformatics and Genomics, Department of Agricultural, Food and Nutritional Science (AFNS) at the University of Alberta; and Dr. Changxi Li with Agriculture and Agri-Food Canada.
With money and great minds in place, the team set out to attain three main objectives.
“With all the genotyping and sequencing done globally and through the 1000 Bull Genomes Project, over 34 million genomic variants in the bovine genome had been discovered, but no one really knew what they were related to,” said Dr. Basarab. “Our first goal was to screen those genomic variants and identify those with the highest probability of having functional impact on traits of interest to the beef industry, which were primarily growth, feed efficiency and carcass traits. This work was led by Stothard’s team.”
Ready, aim, breed
Armed with new information on genomic variants and new statistical approaches, the project’s second objective was applying that data to improve the accuracy of molecular breeding values for ten traits. In addition to feed efficiency and carcass traits such as backfat thickness, marbling score, carcass weight and tenderness, they targeted dry matter intake, body weight, growth and residual feed intake.
Since more precise molecular breeding values mean more profits for producers, Dr. Basarab and his colleagues sought to raise the accuracy from the starting base of 10-15 per cent or less to greater than 35 per cent.
“Our third goal began with the premise that we now have these molecular breeding values with improved accuracy, but we really don’t select on any of those ten traits individually,” said Dr. Basarab. “We select on many traits for a given purpose, such as feeder cattle profitability, good lifetime productivity and fertility of replacement heifers.”
With that in mind, researchers aimed to develop two multi-trait selection indexes for commercial cattle. More specifically, they wanted indices that performed well for crossbred cattle, as they account for greater than 95 per cent of beef production in Canada.
With the desired outcomes clearly defined, it was time to get to work, and the most challenging elements still lay ahead. Like the start of a new school year, however, the best was yet to come.