Genome-Wide Association Studies on the Autosomes and Chromosome X Uncover Genetic Basis of Reproductive Traits in...

Reproductive efficiency is a fundamental determinant of productivity in pig breeding programs. However, the role of the X chromosome in shaping the genetic basis of reproductive traits remains underexplored. To address this problem, Genome-Wide Association Studies were conducted to explore the genetic basis of reproductive traits in Yorkshire pigs. We collected data from 2659 Yorkshire sows, focusing on four reproductive traits across the first three parties. Statistical analyses included principal component analysis, estimation of genetic parameters, and mixed linear model association to identify SNPs and candidate genes. Heritability estimates (h²) ranged from 0.037 (TLWT_BA_P1) to 0.215 (TNB_P3). Genome-wide association analysis identified 23 significant SNPs and candidate genes, including several putatively significant X-linked genes; however, only a single X-linked locus was significantly associated with one trait. These findings demonstrate that, for 9 of the 12 parities, the proportion of total heritability attributable to X-linked variation was 0-2.7%. For the remaining three parities, the corresponding proportions were 8.4%, 21.5%, and 50.9%, while autosomes accounted for most of the genetic variation. In all but one trait, heritability estimated from X-linked GRMs was not significantly different from zero, highlighting the importance of incorporating X-linked information into genomic selection strategies for improving reproductive efficiency in pigs.