Exploiting Whole Genome Sequence Data for the Identification of Causal Trait Variants in Cattle

Abstract Text: Sequence data were generated from 157 animals of the Fleckvieh population. A pre-phasing based approach was used to impute genotypes for 21,045,178 polymorphic sites into 10,363 target animals genotyped with high-density arrays. Imputed sequence variants were used in an association study with daughter-derived phenotypes for milk fat percentage. The association study identified ten QTL controlling fat percentage in Fleckvieh cattle. Two postulated causal variants in the DGAT1 and GHR genes yielded the most significant association signals. Sequence-based association studies for udder conformation traits demonstrated a complex genetic architecture of mammary gland development in cattle. The association studies identified eight, six and seven QTL underlying udder depth, teat length and teat thickness, respectively. Imputed sequence variants captured genetic effects at a better resolution than array-based genotypes. However, even when considering large-scale imputed sequence variants, a significant fraction of the heritability remains “missing”.

Keywords: cattle, whole-genome sequencing, QTL, causal variants