Abstract #750
Section: Breeding and Genetics
Session: Breeding and Genetics: Application and methods - Dairy II
Format: Oral
Day/Time: Wednesday 2:30 PM–2:45 PM
Location: Panzacola F-4
Session: Breeding and Genetics: Application and methods - Dairy II
Format: Oral
Day/Time: Wednesday 2:30 PM–2:45 PM
Location: Panzacola F-4
# 750
Distribution of runs of homozygosity and its association with inbreeding depression in United States and Australia Jersey cattle.
Jeremy T. Howard*1, Christian Maltecca1, Mekonnen Haile-Mariam2,3, Ben J. Hayes2,3, Jennie E. Pryce2,3, 1North Carolina State University, Raleigh, NC, 2Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia, 3La Trobe University, Bundoora, Victoria, Australia, 4Biosciences Research Division, Bundoora, Victoria, Australia.
Key Words: run-of-homozygosity, genome-wide association study, inbreeding depression
Distribution of runs of homozygosity and its association with inbreeding depression in United States and Australia Jersey cattle.
Jeremy T. Howard*1, Christian Maltecca1, Mekonnen Haile-Mariam2,3, Ben J. Hayes2,3, Jennie E. Pryce2,3, 1North Carolina State University, Raleigh, NC, 2Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia, 3La Trobe University, Bundoora, Victoria, Australia, 4Biosciences Research Division, Bundoora, Victoria, Australia.
Differences in environment, management practices or selection objectives have led to a variety of choices being made in the use of dairy sires between countries. This may result in variation in selection intensity across the genome and could result in detectable differences in patterns of genome-level homozygosity between populations and consequently affect inbreeding depression differently across populations. The objective of the study was to characterize the frequency of homozygosity and its relationship with regions associated with inbreeding depression in Jersey dairy cattle from the United States (US) and Australia (AU). Genotyped cows with phenotypes on milk, fat and protein yield (n = 6,751 US; n = 3,974 AU) and calving interval (n = 5,816 US; n = 3,905 AU) were utilized in a 2-stage analysis. A run of homozygosity statistic (ROH4Mb), counting the frequency of a SNP being in a ROH of at least 4 Mb, was calculated across the genome. In the first stage residuals were obtained from a model that accounted for the additive genetic as wells as fixed effects. In the second stage these residuals were regressed on ROH4Mb using a single marker regression model or a machine-learning tree based regression algorithm (gradient boosted machine). The relationship between ROH4Mb and the SNP effect of a region for each trait was further characterized based on sliding window (500kb) direct genomic value (DGV) derived from a Bayesian LASSO analysis. The ROH4Mb effects were estimated by regressing residuals from the 2-stage approach on ROH4Mb and SNP effects estimated by regressing residual deviations from a model including only fixed effects on SNP markers. Genomic regions across multiple traits were found to be associated with ROH4Mb on BTA13, BTA23 and BTA25 for the US population and BTA3, BTA7, BTA17 for the AU population. Furthermore, multiple potential epistatic interactions were characterized. Lastly, the covariance between ROH4Mb and the SNP effect of a region depended on the genome region, with positive covariances in some regions
Key Words: run-of-homozygosity, genome-wide association study, inbreeding depression
