A Gene Network Inferred from Genome-wide Association: Prioritization of QTLs Associated with Tropical Cattle Reproduction

Abstract Text: We derived nine gene networks from 32 genome-wide association studies (GWAS) using 3,270 genes that harbor SNP with pleiotropic effects across these association analyses. These GWAS focused on reproduction-related phenotypes that were measured in male and female Brahman and Tropical Composite cattle. We found variable numbers of significant and correlated co-association SNP, ranging from 9,516 pairs in the cow network to 146,819 in the Tropical Composite bull network. To reduce the dimension of the analyses, we devised the Always Correlated Network, which included only gene-pairs that were significantly co-associated and correlated in all nine networks. Genes within this network were mostly organized per chromosome, but linkage disequilibrium did not fully explain the topology. Several genes that were identified had biological roles in reproductive physiology that linked to their potential pleiotropic effect and set them as candidates for further analyses.

Keywords: Beef cattle, Puberty, Insulin-like growth factor 1