Analysis of runs of homozygosity from next generation sequence data in Canadian dairy cattle

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Cattle breeders commonly estimate inbreeding coefficients by calculating the degree of parental relatedness using pedigree information, and, more recently, SNP data. The rate of inbreeding in dairy cattle populations has increased in recent years, and will likely continue to increase steadily as genomic selection intensifies. In Canada, Stachowicz et al. (2011) found that both Jersey and Holstein populations have very limited gene pools and already suffer from negative effects of accumulation of inbreeding and genetic diversity loss. The authors suggest that the rapid decrease in generation interval through genomic selection will cause an even faster accumulation of inbreeding over time. They concluded that a need exists for managing selection and mating decisions to control future inbreeding. Using current genomic information, we propose the use of new genomic tools to better understand the mechanisms of inbreeding in Canadian dairy populations and to re-evaluate appropriate rates of inbreeding. This research project involves 3 stages: (1) analysis of genomic inbreeding in Canadian dairy breeds using both array and sequence information, and characterisation of regions of homozygous loci, including rate and functional severity of deleterious and neutral variants within runs of homozygosity, (2) understanding the consequences of genomic inbreeding through genome-wide association analyses using the regions of homozygosity identified, (3) integration of new knowledge into selection strategies to help manage genomic inbreeding based on simulation results. We propose that the currently available genomic information provides new possibilities for monitoring and controlling the frequency of deleterious recessive alleles and haplotypes.