Exploiting single-marker and haplotype-based genome-wide association studies to identify QTL for the number of teats in Italian Duroc pigs

Abstract

The number of teats is a morphological trait of high economic relevance for the pig industry. Here, to dissect the genomic architecture of this trait in the Italian Duroc pig population, we present the results of genome-wide association studies in this Italian heavy pig breed. A total of 1,162 pigs, for which the number of teats was recorded, was genotyped with two high-throughput single nucleotide polymorphism (SNP) genotyping platforms (60 K and 70 K). Genome-wide association analyses were based on a single-marker approach and on a haplotype-based approach. Two quantitative trait loci (QTL) affecting the number of teats were identified. The most significant QTL, identified by the single-marker analysis and confirmed by the haplotype-based method, was located on Sus scrofa chromosome (SSC) 7, in the region of the vertnin (VRTN) gene. Suggestively associated markers (SNPs and haplotypes) were located on SSC10, in the region of the FERM domain containing 4A (FRMD4A) gene, the second identified QTL. These findings confirm previous results obtained in a few other Duroc populations. Overall, this study further supported the important role of variability in the VRTN gene region in affecting the number of teats in pigs. Moreover, the results also indicated that this trait in the Italian Duroc breed, as in many other pig breeds, is affected by few QTL, with the contribution of many other genetic factors with small effects, following the classical theory of quantitative traits.