Identifying functional gene variants and non-additive effects to enhance the power of genomic selection of purebred pigs for crossbred performance

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Genetically improving lean meat yield and pork quality is a key approach for the Canadian swine industry to enhance global competitiveness and overall profitability. Genomically enhanced estimated breeding values (GEBVs) are based on DNA marker genotypes and effects. GEBVs are used to increase the rate of genetic improvement for production traits, particularly for those that are difficult and/or expensive to measure, such as carcass yield and pork quality. The overall goal of this project is to improve the GEBVs for these traits through the integration of functional gene variants and better estimates of the overall genetic effect (additive and non-additive elements) by generating and using whole genomic sequence information and low density SNP panels. This work, a collaboration with a major Canadian and international pig breeding company will develop advanced knowledge and technology, which will benefit both the academic and industry partners. With this project, reduced genotyping cost (due to imputation) and enhanced power of genome prediction will significantly increase the adoption of genomic technologies in the Canadian swine industry. The delivery of novel genomic tools and techniques (e.g. sequence imputation, mating allocation), and experienced geneticists will improve Canadian pig breeding and selection programs . In addition, a large set of genomic data resources will be generated and shared, which represent valuable information for future genomic research in pigs. Knowledge of functional gene variants will also lead to new insights for the genomic architecture and underlying biology impacting pork yield and quality, and ultimately result in increased returns to the economic benefit of the swine industry.