Animal breeders blazed the trail on complex traits

Who wants canola with heat tolerance to protect flowers and reproduction during summer heatwaves? We do! Who wants canola with enhanced drought tolerance, water use efficiency and nutrient use efficiency? We do!

Many genes manage these complex traits, which makes them hard to tackle. But animal scientists figured out two decades ago how to select for complex traits. Canola researchers are catching on.

Theo Meuwissen, animal scientist at the Research Institute of Animal Science and Health in The Netherlands, was a trailblazer. In an article, “Genomic selection: A paradigm shift in animal breeding” in the journal Animal Frontiers, Meuwissen wrote that complex traits in livestock are often determined by thousands of genes and the effect of each individual gene was “usually too small to be statistically significant and so were ignored.” Meuwissen helped introduce the idea of genomic selection, which estimates the effect of all genes within a trait, not just the statistical significance (or lack thereof) of one gene at a time. The Animal Frontiers article says genomic selection feeds on three technological breakthroughs: the development of the genomic selection technology, the discovery of massive numbers of genetic markers, and high-throughput technology to genotype animals for thousands or hundreds of thousands of markers in a cost-effective manner.

The Global Institute for Food Security (GIFS) at the University of Saskatchewan in Saskatoon recently hired Hakimeh Emamgholi Begli, a quantitative geneticist, to work on genomic selection in common Western Canadian crops, including canola, wheat, barley and peas. Emamgholi Begli will use data analytics to find the package of genes connected with complex traits, and estimate the heritability and genetic and phenotypic corrections between multiple traits.

Nancy Tout, chief scientific officer with GIFS, says Emamgholi Begli’s background is a “source of strength for our team and the plant science industry at large,” adding: “The animal industry has really embraced genomic selection and the modern breeding toolkit to significantly enhance their rates of genetic gain and across multiple traits.”

“The animal industry has really embraced genomic selection and the modern breeding toolkit to significantly enhance their rates of genetic gain and across multiple traits.”

– Nancy Tout

Before coming to GIFS, Emamgholi Begli worked on application of genomic selection in poultry in Europe. She also worked at the Centre for Genetic Improvement of Livestock at the University of Guelph. At Guelph, she investigated different genomic methods that would improve egg production over the laying life of a turkey hen. She brings those skills to GIFS.

GIFS hosted a webinar describing the potential benefits of genomic selection, a key part of its new accelerated breeding program. In the webinar, presenters provided examples of genomic selection benefits from Australia.

DataGene, a division of Dairy Australia, used genomic selection to improve complex traits in fertility, feed efficiency, heat tolerance, mastitis resistance and gestation length in dairy cows. From 2010 to 2020, rapid introduction of numerous complex traits caused a sharp uptick in balanced performance index (BPI) for Australian dairy cattle. As noted on the Dairy Australia website, BPI measures “genetic merit for the combination traits that contribute to a profitable business.”

The challenge with plants

Emamgholi Begli says challenges specific to plants include the complexity of traits influenced by environmental factors. “With plants, we may find complex traits that work in one environment will not produce the same in another environment,” she says. “In comparison, animals benefit from simpler genetic architectures and controlled breeding environments, making genomic selection implementation relatively straightforward.”

Also with plants, some complex traits are not easily passed from one generation to the next. These factors complicate the accuracy of genomic predictions and require robust computational models and large-scale genomic data. Part of the genomic selection process is to work with complex traits that are “heritable”, find markers for the important traits, and use rapid analysis to check seeds for the presence of those markers. That way only seeds with the trait go on to greenhouse or field trials.

“Despite these challenges, genomic selection is a promising technique in plant breeding,” Emamgholi Begli says. “With genomic selection, better selections are hitting the field at a better rate.”

Genomic selection will help Western Canadian farmers “close the productivity gap”.
– Nancy Tout

In a 2023 report, Farm Credit Canada (FCC) senior economist Isaac Kwarteng wrote: “The low-hanging fruits are gone for growing our productivity. We recorded sensational increases in average annual productivity growth from 1971 to 2000, then hit a plateau.” Canadian agriculture productivity growth was 1.4 per cent from 2011 to 2020 and is forecast at 1.0 per cent for 2021 to 2030, Kwarteng reports. To paraphrase the report’s conclusions: The decline in productivity growth represents a major challenge, but also presents Canada with an “amazing opportunity”.

Putting its money where its mouth is, FCC earlier this year contributed $5 million to the GIFS accelerated breeding program. It wants to see Canadian breeders embrace the techniques deployed for over 20 years in dairy and for more than a decade in crops such as corn and soybean through large corporations. “The FCC Accelerated Breeding Program at GIFS will provide public and private breeders access to the same technologies not routinely available for crops and livestock important to Canada,” FCC said in its announcement.

GIFS works with several dozen public and private organizations to accelerate innovation across the value chain, Tout says, but specific agreements are confidential.

We do know that Emamgholi Begli is doing work on canola. “We’ve established our capacity, capabilities and competencies to launch our accelerated breeding program using our established expertise on canola,” Emamgholi Begli says, “and are now excited to expand this across a number of crops, including pulses and cereals.”

Chad Koscielny, Corteva’s North America canola breeding lead, describes how private canola seed companies are also using the technology. “Corteva has made remarkable gains in corn using new breeding technologies. We’re applying the same technology to our canola breeding program and are seeing similar promising results within our R&D pipeline,” Koscielny says.

Corteva has been using genomic selection to identify and select for complex traits in canola for several years now and Koscielny says “the progress has been exciting to see.”