Genome-wide association study discovers new QTL and candidate genes on SSC2 associated with total teat number in Large White × Tongcheng crossbred pigs

Teat number is an economically important trait in pigs because it is relevant to reproduction efficiency and thus production profitability. In this study, a genome-wide association study (GWAS) was performed with genotyping by genome resequencing, which identified six significant SNPs (single nucleotide polymorphisms) on Sus scrofa chromosome 2 (SSC2) and SSC7 for total teat number using 888 Large White × Tongcheng crossbred pigs. The Bayesian fine-mapping further defined two QTL (quantitative trait loci) with locations of 18.32–19.08 and 21.18–22.11 Mb on SSC2, and one QTL spanned an interval of 97.14–97.91 Mb on SSC7, respectively. The first SSC2 QTL region harbors four candidate genes TTC17, API5, miR-129-2 and HSD17B12. The SSC7 QTL region include two reported candidate genes, VRTN and ABCD4. The average teat numbers are 12.42 ± 1.38, 13.52 ± 1.10 and 13.87 ± 1.03 for TT, TA and AA genotypes of rs340400902 on SSC2, respectively. The T allele of rs340400902 on SSC2 in Large White × Tongcheng crossbred pigs was found to originate from Tongcheng pigs. These findings provides SNPs and candidate genes for the genetic improvement of teat number in pigs.