IDENTIFICATION OF LOCI ASSOCIATED WITH ECONOMICALLY IMPORTANT TRAITS IN CATTLE
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Genomic selection provides the cattle industry with new opportunities to improve animal health and production. The objective of this dissertation was to identify quantitative trait loci (QTL), genes, gene sets and regulators of genes associated with susceptibility to bovine respiratory disease (BRD) in beef and dairy cattle, fertility in beef cattle, and polymelia in a Holstein calf. BRD is a complex disease in cattle initiated by stressful events in conjunction with the presence of viral and bacterial pathogens in the respiratory tract. In this study, 2,762 Holstein calves (1,379 cases and 1,383 controls) from California and New Mexico along with 2,000 beef cattle (1,004 cases and 996 controls) from Colorado and Washington were sampled from commercial facilities. Single nucleotide polymorphism - based gene set enrichment analysis (GSEA-SNP) identified six gene sets with 104 leading edge genes (LEGs) and nine gene sets with 231 LEGs in dairy and beef populations, respectively. A fine mapping study with imputation and custom genotyping in the same California population identified 29 additional dystonin variants that are associated with BRD susceptibility. Embryonic loss is another complex trait that was investigated to identify loci and genes associated with infertility. Early pregnancy loss was investigated in 80 Angus crossbred heifers classified as high fertile (n = 30) and subfertile (n = 55), based on day 28 pregnancy outcomes to serial embryo transfer. Genome wide association analysis (GWAA) identified 22 QTL, and GSEA-SNP revealed nine genes sets with 253 LEGs. Further, network analysis revealed 674 upstream regulators and 774 master regulators associated with fertility. An additional study involved a single case of extra limbs (polymelia) in a Holstein calf which was compared with 2,650 control animals. The GWAA identified loci on chromosomes 13 and 10 associated with polymelia and 79 candidate genes that were homozygous only in the presence of polymelia. The identification of loci associated with BRD, fertility and polymelia offers new opportunities for producers to select cattle that have improved health and performance.