A Whole Genome Sequencing-Based Genome-Wide Association Study Reveals the Potential Associations of Teat Number in Qingping Pigs

SIMPLE SUMMARY: Teat number is important for the mothering ability of a sow, but this trait has seldom been investigated by high-depth genomic data-based genome-wide association study (GWAS). Here, we performed GWAS for the teat number-related traits in 100 Chinese native Qingping pigs by recording their left and right teat numbers and analyzing their genetic variations through 10-fold whole-genome sequencing. T-Box Transcription Factor 3 (TBX3) on Sus scrofa chromosome (SSC) 14 and Wnt signaling pathway are revealed to be associated with teat number-related traits, with important roles in mammary gland morphogenesis and development. ABSTRACT: Teat number plays an important role in the reproductive performance of sows and the growth of piglets. However, the quantitative trait loci (QTLs) and candidate genes for the teat number-related traits in Qingping pigs remain unknown. In this study, we performed GWAS based on whole-genome single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) for the total number of teats and five other related traits in 100 Qingping pigs. SNPs and Indels of all 100 pigs were genotyped using 10× whole genome resequencing. GWAS using General Linear Models (GLM) detected a total of 28 SNPs and 45 Indels as peak markers for these six traits. We also performed GWAS for the absolute difference between left and right teat number (ADIFF) using Fixed and random model Circulating Probability Unification (FarmCPU). The most strongly associated SNP and Indel with a distance of 562,788 bp were significantly associated with ADIFF in both GLM and FarmCPU models. In the 1-Mb regions of the most strongly associated SNP and Indel, there were five annotated genes, including TRIML1, TRIML2, ZFP42, FAT1 and MTNR1A. We also highlighted TBX3 as an interesting candidate gene for SSC14. Enrichment analysis of candidate genes suggested the Wnt signaling pathway may contribute to teat number-related traits. This study expanded significant marker-trait associations for teat number and provided useful molecular markers and candidate genes for teat number improvement in the breeding of sows.