Regions impacting inbreeding depression and their association with additive genetic effects for United States and Australia jersey cattle. — ASN Events
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  2. Concurrent 2 - Reproduction, behaviour & health I
  3. Regions impacting inbreeding depression and their association with additive genetic effects for United States and Australia jersey cattle.

Regions impacting inbreeding depression and their association with additive genetic effects for United States and Australia jersey cattle. (#8)

Jeremy T Howard 1 , Mekonnen Haile-Mariam 2 3 , Jennie E Pryce 2 3 , Christian Maltecca 1
  1. North Carolina State University, Raleigh, NC, United States
  2. La Trobe University , Bundoora , Victoria , Australia
  3. Department of Economic Development, Jobs, Transport and Resources and Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia

The advent of dense genotype platforms allow for the identification of specific regions that give rise to inbreeding depression and characterize their relationship with the additive effect of that region. Utilizing a run of homozygosity (ROH) metric the first study objective is to identify regions having an impact on inbreeding depression for United States (US) and Australia (AU) Jersey cows. The second objective is to determine the relationship between the additive and ROH SNP effects. Genotyped cows with phenotypes on milk yield traits (US=6751; AU=3974) and calving interval (US=5816; AU=3905) were utilized. A ROH based metric (ROH4Mb) was calculated across the genome. Residuals from a model that accounted for the fixed and additive genetic effects were regressed on ROH4Mb using a single marker regression or a machine-learning tree based model. The relationship between ROH4Mb and additive effect was characterized based on sliding window (500kb) direct genomic value derived from a Bayesian-LASSO analysis. Genomic regions across multiple traits were found to be associated with ROH4Mb for the US on BTA13, BTA23 and BTA25 and AU on BTA3, BTA7 and BTA17. Multiple potential epistatic interactions were characterized. The covariance between ROH4Mb and the additive effect depended on the genomic region.

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