204 Genomics of age at puberty in gilts

Abstract

Abstract Our previous research demonstrated that age at puberty is characterized by moderate heritability and is an early pre-breeding indicator of sow fertility. Early selection of gilts, based on genomic prediction of age at puberty and fertility in general, is considered a potential approach to reduce sow culling. Phenotypes, genotypes and tissues from UNL resource population (n > 1,700) were used in initial genome-wide association to identify regions of the genome associated with age at puberty. The proportion of phenotypic variation for age at puberty explained by the Porcine SNP60 BeadArray was 27.3%, with top genomic regions responsible for relatively small effects. The top 1-Mb windows (1%) explained 6.7% of the genetic variation with one window located on SSC2 (12–12.9 Mb) displaying pleiotropic features, affecting both age at puberty and litter size. These top genomic regions were oversaturated with new genetic variants discovered by deep genomic and RNA (arcuate nucleus) sequencing, which were integrated in SowPro90, a custom Affymetrix SNP array. Using a subset of sows representing extremes of the distribution for age at puberty (n = 283) and genotyped with the SowPro90 led to identification of a SNP in the proximal promoter of the UBE2L6 (SSC2, 13.3Mb; F = 13.39; P = 0.0003), a gene known to modulate function of ISG15, a marker for pregnancy. This novel SNP, which exceeded the effect of the original top SNP in the region (DIAS0004771; F = 6.98), explained 6.8% of the proportion of phenotypic variance. Identification of functional polymorphisms that influence age at puberty could lead to improvements in the accuracy of genomic prediction while reducing sow replacement rates. This project was supported by AFRI Competitive Grant no. 2013-68004-20370 from the USDA-NIFA.