Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs

SIMPLE SUMMARY: Improving the reproductive performance of sows is a paramount goal in breeding programs. The number of teats is significantly associated with the reproductive performance of sows, with quantitative trait loci (QTL) related to porcine papilla number traits identified across almost all chromosomes, and with candidate genes proposed. In this study, we analyzed the total teat number traits of 1518 Duroc × (Landrace × Yorkshire) (DLY) pigs and performed genotyping using a 50K chip. By screening SNP loci and related genes, this study aimed to identify genetic factors affecting the number of teats in DLY pigs and to facilitate future breeding programs aimed at improving this trait. ABSTRACT: The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.