Genome-Wide Association Study Identified a Quantitative Trait Locus and Two Candidate Genes on Sus scrofa Chromosome 2 Affecting Vulvar Traits of Suhuai Pigs

Vulvar size and angle are meaningful traits in pig production. Sows with abnormal vulva generally show reproductive disorders. In order to excavate candidate loci and genes associated with pig’s vulvar traits, 270 Suhuai pigs with vulvar phenotype were genotyped by a porcine single nucleotide polymorphisms (SNP) Chip. Then, Chip data were imputed using resequenced data of 30 Suhuai pigs as a reference panel. Next, we estimated the heritability and performed a genome-wide association study (GWAS) for vulvar traits. The heritabilities for the traits vulvar length (VL), vulvar width (VW) and vulvar angle (VA) in this pig population were 0.23, 0.32 and 0.22, respectively. GWAS based on Chip data identified nine significant SNPs on the Sus scrofa chromosomes (SSC) 2, 7, 9 and 13 for VL or VW. GWAS based on imputed data identified 11 new quantitative trait loci (QTL) on SSC1, 2, 7, 8, 9, 11, 13, 16 and 17 for VL or VW. The most significant QTL for VL on SSC2 were refined to a 3.48–3.97 Mb region using linkage disequilibrium and linkage analysis (LDLA). In this refined region, FGF19 and CCND1, involved in the development of the reproductive tract, cell growth and vulvar cancer, could be new candidate genes affecting VL. Our results provided potential genetic markers for the breeding of vulvar traits in pigs and deepened the understanding of the genetic mechanism of vulvar traits.