Investigation of regions impacting inbreeding depression and their association with the additive genetic effect for United States and Australia Jersey dairy cattle

Abstract

Background: Variation in environment, management practices, nutrition or selection objectives has led to a variety of different choices being made in the use of genetic material between countries. Differences in genome-level homozygosity between countries may give rise to regions that result in inbreeding depression to differ. The objective of this study was to characterize regions that have an impact on a runs of homozygosity (ROH) metric and estimate their association with the additive genetic effect of milk (MY), fat (FY) and protein yield (PY) and calving interval (CI) using Australia (AU) and United States (US) Jersey cows. Methods: Genotyped cows with phenotypes on MY, FY and PY (n = 6751 US; n = 3974 AU) and CI (n = 5816 US; n = 3905 AU) were used in a two-stage analysis. A ROH statistic (ROH4Mb), which counts 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 portion explained by the estimated breeding value. In the second stage, these residuals were regressed on ROH4Mb using a single marker regression model and a gradient boosted machine (GBM) algorithm. The relationship between the additive and ROH4Mb of a region was characterized based on the (co)variance of 500 kb estimated genomic breeding values derived from a Bayesian LASSO analysis. Phenotypes to determine ROH4Mb and additive effects were residuals from the two-stage approach and yield deviations, respectively. Results: Associations between yield traits and ROH4Mb were found for regions on BTA13, BTA23 and BTA25 for the US population and BTA3, BTA7, BTA17 for the AU population. Only one association (BTA7) was found for CI and ROH4Mb for the US population. Multiple potential epistatic interactions were characterized based on the GBM analysis. Lastly, the covariance sign between ROH4Mb and additive SNP effect of a region was heterogeneous across the genome. Conclusion: We identified multiple genomic regions associated with ROH4Mb in US and AU Jersey females. The covariance of regions impacting ROH4Mb and the additive genetic effect were positive and negative, which provides evidence that the homozygosity effect is location dependent.