Utilizing Genetics to Improve Cattle Efficiencies and Evaluate Economically Important Traits and Conditions

Allison Louise Herrick

doi:10.7273/000007894

The identification and use of genetic regions is a technique utilized throughout the cattle industry to select for improved populations, commonly using genomic selection. The objective of this dissertation was to identify loci, genes, gene sets, and leading-edge genes associated with cryptorchidism in Wagyu cattle and bovine respiratory disease (BRD) in Holstein calves and to evaluate economic and environmental impacts on commercial dairies due to the use of genomic selection techniques. Cryptorchidism is a condition where one or both testes fail to descend into the scrotum, leading to reductions in fertility. Wagyu cattle have a small effective population size and large inbreeding coefficients, as well as some families with a higher proportion of cryptorchidism. To examine any potential genetic regulators of cryptorchidism, a population of 18 individuals from a related family were genotyped. Haplotype association and genome wide association analyses (GWAA) were performed, identifying 218 haplotypes that trended towards an association and three loci moderately associated with cryptorchidism. To assess long-term impacts of genomic selection on environmental outputs and dairy profitability, a ten-year Markov chain model evaluated differences between three selection scenarios. The study compared traditional, single-trait genomic, and multi-trait genomic selection scenarios, where the dairies reached a non-fluctuating state and prioritized maximum profit. Farm profit was 50% and 64% higher in single and multi-trait genomic selection scenarios compared to traditional selection. Moreover, they had approximately 7% less methane, 10% less phosphorus, and 13% less nitrogen productions compared to traditional selection. Other factors, including improved milk production and reproductive performances were also observed, due to the higher selection intensity of these traits, especially in the multi-trait genomic selection scenario. The final two studies examined BRD, which is a respiratory infection among cattle due to various bacteria and viruses. Both studies performed GWAA and gene set enrichment analyses using single nucleotide polymorphisms as gene proxies (GSEA-SNP) on a pre-weaned population (0-60 days of age) and a post-weaned population (61-421 days of age). The Pacific Northwest population included 518 pre-weaned cases and 3,655 controls and the post-weaned portion had 2,001 cases and 3,210 controls. The GWAA identified 13 strongly associated loci and 26 positional candidate genes with associated markers within them for the pre-weaned population. The post-weaned population identified 52 strongly associated loci across additive, dominant, and recessive models and 56 positional candidate genes. The GSEA-SNP identified a single gene set with 86 leading-edge genes and seven gene sets with 162 unique leading-edge genes for the pre- and post-weaned populations, respectively. The Southern population also genotyped pre-weaned calves (2,147 cases and 14,219 controls) and post-weaned calves (5,607 cases and 12,242 controls). The pre-weaned GWAA identified 62 loci across the three inheritance models and 123 unique positional candidate genes. The post-weaned GWAA identified 181 associated loci and 185 unique positional candidate genes. The GSEA-SNP found 12 enriched gene sets with 126 leading-edge genes for the pre-weaned population and 63 gene sets with 849 unique leading-edge genes for the post-weaned population. Loci associated with cryptorchidism and BRD, as well as evaluating long-term benefits of commercial genomic selection, highlight the opportunities for producers to select healthier populations of cattle while also improving their financial and environmental sustainability.

Utilizing Genetics to Improve Cattle Efficiencies and Evaluate Economically Important Traits and Conditions

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