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Identification and validation of candidate genes for heat tolerance in Australian Holstein dairy cattle.

E. K. Cheruiyot




Identification and validation of candidate genes for heat tolerance in Australian Holstein dairy cattle.
E. K. Cheruiyot*1,2, M. Haile-Mariam1, B. G. Cocks1,2, I. MacLeod1, J. E. Pryce1,2. 1Agriculture Victoria Research, Department of Jobs, Precincts and Regions Melbourne, Australia, 2School of Applied Systems Biology, La Trobe University Melbourne, Australia.

Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot conditions and is now a trait of economic relevance in dairy systems worldwide. Understanding the genetic basis for heat tolerance is an important part of the strategy to breed for cattle adapted to warmer environments. We sought to identify and validate candidate genes involved in heat tolerance in Australian Holstein cattle using 50K SNP chip and imputed whole-genome sequences (WGS) in 2 data sets: cows (n = 20,623) and bulls (n = 1,622). The WGS was imputed using Run 7 of the 1000 Bull Genome Project based on the ARS-UCD1.2 reference genome. After quality checks, approximately 45K and 15 million SNPs remained for analysis from the 50K chip and the WGS, respectively. The heat tolerance phenotypes that were used for this study were derived from test-day milk, protein and fat yield data of cows that calved between 2003 to 2017 and represent the response of cows to heat stress. For the 3 milk traits, the slope which measures change in milk yield due to variability in temperature-humidity index from reaction norm models calculated for individual animals after accounting for known fixed effect was used as phenotype in association analysis using GCTA software. We used cows for discovery and bulls that were not sires of the cows for validation. Our results point to the polygenic nature of heat tolerance, with no variants surpassing a significance threshold of P < 1.0 � 10—6 for 50K SNP data. While we detected some associations when the threshold was set at P < 1.0 � 10—3, there were high false discovery rates. In contrast, we detected multiple variants with P < 1.0 � 10—6 across the genome using WGS, suggesting greater power compared with 50K SNP data. Across our cow and bull validation set, we confirmed several candidate genes, including some that have been reported previously. Our results are preliminary and could be useful to enhance the reliability of heat tolerance genomic breeding values of Australian Holstein cattle which is currently about 38%. This will be investigated in a further study.

Keywords: heat tolerance, dairy cattle, whole-genome sequences (WGS).

Biography: Evans Cheruiyot is currently a second-year PhD candidate at La Trobe University, Melbourne, working on the genetics of heat tolerance in dairy cattle. Previously, Evans graduated from the University of Nairobi, Kenya in 2017 with an MSc degree in Animal Genetics and Breeding.