Genome-wide Association Study for Number of Vertebrae in an F2 Large White × Minzhu Population of Pigs

ABSTRACT Porcine carcass that is approximately 800 mm long may be expected to have one additional vertebra. Therefore, the number of vertebrae in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 593 F2 Large White × Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study identified 39 significant single-nucleotide polymorphisms (SNPs) on the chromosomes SSC1 and SSC7. An 8.82-Mb region that contained all 21 significant SNPs on SSC1 harbored the gene NR6A1 , previously reported to influence the number of vertebrae in pigs. The remaining 18 significant SNPs on SSC7 were concentrated in a 4.56-Mb region, which was within the quantitative trait loci interval for number of vertebrae. A haplotype sharing analysis refined the locus to a segment of ∼637 Kb. The most significant SNP, SIRI0001067, was contained in this refined region on SSC7 and located in one of the introns of TGFB3 . As TGFB3 influences the development of vertebrae in mammalian embryos, the gene may be another strong candidate for the number of vertebrae in pigs.