Understanding the genomic basis of health, efficiency, productivity and welfare of farm animals

点击翻译按钮获取中文摘要

Livestock breeders commonly estimate inbreeding coefficients by calculating the degree of parental relatedness using pedigree information, and, more recently, using single nucleotide polymorphism (SNP) data. The rate of inbreeding in livestock populations has increased in recent years, and will likely continue to increase steadily as genomic selection intensifies - an unavoidable consequence of intense directional selection. The overall objective of this research program is to understand and manage the phenotypic and genotypic variability of runs of homozygosity in Canadian livestock using both array data and next-generation sequence data in order to improve animal robustness and manage the potential detrimental effects of inbreeding. We propose the use of new genomic tools to better understand the mechanisms of inbreeding in Canadian livestock populations and to re-evaluate appropriate rates of inbreeding. Firstly, patterns and lengths of chromosomal segments leading to runs of homozygosity with both array data and next-generation whole-genome sequence data under consideration of recombination loci will be identified, including aspects of origin disequilibrium (i.e. the likelihood of one haplotype being transmitted being higher than that of the other). Secondly,  the rate and functional deleterious (or advantageous) severity of homozygous regions will be identified. Thirdly, genome-wide association studies on runs of homozygosity and inherited chromosomal segments affecting various traits of economic importance to the Canadian dairy industry will be identified. Finally, the observed characteristics of chromosomal inheritance in Canadian Holsteins will be used to test various selection scenarios and to integrate new knowledge of genomic inbreeding into mating strategies by creating software tools to help manage inbreeding. We propose that currently available genomic information provides new possibilities for monitoring and controlling the frequency of deleterious recessive alleles and haplotypes.  The ultimate goal of this research is to improve health and welfare of farm animals using genetic and genomic methods, as well as to uncover the relationship between phenotype and genotype in livestock. Understanding how desirable and undesirable traits are controlled at the DNA sequence level has the potential to accelerate the breeding of healthy, disease-resistant animals by several orders of magnitude. The tools and methods developed within this program will not only be able to improve animal health and welfare, reduce antibiotic use in dairy and poultry production, but they will also be specifically designed to be transferable to other livestock species. My hope is that the genomic tools we develop will gain widespread adoption and be used to select healthy animals with high levels of fitness that attain commercial success, require less antibiotics, and have a higher quality of life.