Genome-wide association studies on the Autosomes and Chromosome X uncover genetic basis of reproductive traits in Yorkshire pigs

Background 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. Results To address this problem, 2,659 Yorkshire genotyped sows with 39,048 autosomal and 1,947 X-chromosomal SNPs were analyzed for four reproductive traits: total number born (TNB), number weaned (NWEAN), total litter weight at birth (TLWT_BA), and total litter weight at 21 days (TLWT_D21). After stringent quality control, heritability estimates (\(\:{h}^{2}\)) ranged from 0.037 (TLWT_BA_P1) to 0.215 (TNB_P3). While autosomes accounted for most genetic variation, the X chromosome contributed substantially, explaining nearly half of the total heritability for TNB_P3 and about one-quarter for NWEAN_P2. Genome-wide association analysis identified 23 independent SNPs significantly associated with the traits, pinpointing candidate genes including ARHGEF2, TENM2, ACACA , and RBM10 . Functional enrichment analysis revealed that ARHGEF2, DEFB1, DNAI2 , and SPACA5 were involved in sperm flagellum assembly, cilium organization, and developmental processes. KEGG pathway analysis highlighted the insulin and ErbB signaling pathways, involving ACACA, ARAF, ELK1 , and SHC1 genes. Several candidate genes, including SPACA5, ELK1 , and ARAF , were located on the X chromosome, suggesting potential X-linked regulatory effects on reproductive performance. Conclusions These findings demonstrate the substantial contribution of the X chromosome to the genetic regulation of sow reproductive traits and emphasize the importance of incorporating X-linked information into genomic selection strategies for improving reproductive efficiency in pigs.