Genome-wide association study to identify quantitative trait loci and positional candidate genes affecting sow lifetime productivity traits in Landrace and Yorkshire pigs

Sow lifetime productivity (SLP)-related traits are important because of their close association with overall productivity in the swine industry. Previous studies were limited to single breeds, making it difficult to comprehensively characterise breed-specific genetic architecture underlying SLP-related traits. To address this gap, we simultaneously analysed Landrace and Yorkshire populations to identify genetic factors that commonly or differentially influence these traits. In this study, we conducted a high-resolution genome-wide association study (GWAS) and biological pathway analysis for lifetime number of litters (LNLs) and lifetime production of pigs (LPPs) in Yorkshire and Landrace breeds. A total of 3 912 pigs (2 869 Yorkshire and 1 043 Landrace) were genotyped using the Illumina Porcine SNP60K BeadChip, and the Fixed and random model Circulating Probability Unification method was used for GWAS of these traits. We identified seven single-nucleotide polymorphism (SNP) markers significantly associated with LNL in both breeds (four in Landrace on chromosomes 1, 5, 6, and 17; three in Yorkshire on chromosomes 4, 8, and 14). Additionally, three SNP markers associated with LPP were identified in Yorkshire on chromosomes 4, 9, and 13 at the genome-wide significance level. The high-resolution identification of QTLs for LNL and LPP was substantiated through comprehensive simulation studies. Among the positional candidate genes identified, WDR11 and TENM4 represent particularly novel findings for porcine reproduction: WDR11 is known to cause reproductive disorders through GnRH dysfunction, and TENM4 plays a critical role in early embryonic development and mesoderm formation, with its disruption leading to embryonic lethality and reproductive failure. Biological pathway analysis was performed using the Enrichr database. Three pathways were significantly enriched: cholesterol metabolism, cell adhesion molecules, and oxytocin signalling. These pathways can influence sow reproductive performance and lifetime productivity. Our findings enhance understanding of the genetic architecture of SLP-related traits and these identified SNP markers and their effect sizes provide important information for optimising genomic selection programmes in swine breeding, enabling more accurate prediction of breeding values for SLP and facilitating the development of breed-specific selection strategies to improve reproductive longevity in pigs.