Quantitative trait loci for the number of vertebrae on Sus scrofa chromosomes 1 and 7 independently influence the numbers of thoracic and lumbar vertebrae in pigs

Although quantitative trait loci (QTLs) for number of thoracic-lumbar vertebrae have been identified on Sus scrofa chromosomes (SSCs) 1 and 7, the influence of these QTLs on the thoracic and lumbar vertebrae is not clear. The aim of this study was to identify single nucleotide polymorphisms (SNPs) associated with total number of thoracic-lumbar vertebrae and for each trait (number of thoracic and lumbar vertebrae) separately. A total of 581 individuals from an F2 Large White×Minzhu population were genotyped using an SNP60K chip. Performing a genome-wide association study (GWAS) for total number of thoracic-lumbar vertebrae, 38 significant SNPs were identified in two QTL regions located on SSC1 and SSC7. Performing a GWAS for number of thoracic vertebrae only, 72 significant SNPs were located on SSC7. While performing a GWAS for number of lumbar vertebrae only, 17 significant SNPs were identified on SSC1. Gene mining suggested that the gene encoding orphan nuclear receptor, germ cell nuclear factor (NR6A1) on SSC1 was a strong candidate affecting the number of lumbar vertebrae in pigs. Additionally, genes encoding vertnin (VRTN), prospero homeobox 2 (PROX2), Finkel-Biskis-Jinkins murine osteosarcoma viral oncogene homolog (FOS), and transforming growth factor beta 3 (TGFB3) may be important candidates affecting the number of thoracic vertebrae in pigs. QTLs on SSC1 and SSC7 independently influenced the numbers of thoracic and lumbar vertebrae. These results shed light on the complex genetic background of vertebrae development in pigs.