Integration of Genomic Resources to Uncover Pleiotropic Regions Associated with Age at Puberty and Reproductive Longevity in Sows

Commercial and experimental genetic resources were used to investigate genetic pleiotropic factors that influence age at puberty, litter-size and reproductive longevity. The phenotypes were complemented by high-density genotyping and whole genome and RNA sequencing. The SNPs from Porcine SNP60 BeadArray explained 25.2% of the phenotypic variation for age at puberty and less for litter-size traits or lifetime number of parities (<10%). The top 1% major 1-Mb windows explained 6.7% of the genetic variance for age at puberty and included genes involved in reproductive processes from progesterone secretion to placental development and embryo implantation. Due to differences in linkage disequilibrium in an evaluation data set, the predictive potential of all the SNPs from major 1-Mb windows (12.3-36.8%) was larger compared to the most informative SNPs from these window (6.5-23.7%). The limited capability of the BeadArray was complemented by polymorphisms discovered by genome sequencing of selected sires (n=20, >20X) in order to uncover functional variants responsible for the phenotypic differences. The role of gene expression in explaining variation of age at puberty was assessed by RNA sequencing of the hypothalamic arcuate nucleus in gilts with different pubertal status (n=37). Seventy genes were differentially expressed between early and late pubertal gilts (P_adj<0.1), including genes involved in reproductive processes. We expect that integration of all these approaches will provide an improvement in the accuracy of genomic prediction by employing functional information responsible for the early onset of puberty and reproductive longevity. Supported by. USDA-NIFA AFRI 2013-68004-20370. USDA is an equal opportunity provider and employer.