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Regulatory and coding genome regions are enriched for trait associated variants in dairy cattle
Whole genome sequencing has discovered a large number of genetic variants that can potentially be useful for genomic predictions and GWAS. However, this does massively increase the number of variants that can be included in such analyses. We aim to reduce this number to a subset more likely to be associated with traits based on the underlying biological information by annotating variants from the Bovine HD array and investigate which are enriched or depleted for trait associated variants in a GWAS with 16,500 Holstein and Jersey dairy cattle. While a variance component analysis finds the annotations that explain most of the genetic variance on a per SNP basis. Our results illustrate that functionally annotating SNPs assists with prioritization to a subset more likely to be associated with complex traits reducing the computational overhead and number of variants needed for further testing.
Keywords:
Genome annotation
Enrichment/Depletion for Trait Associated SNP
