A Genome-Wide Association Study of Rib Number and Thoracolumbar Vertebra Number in a Landrace × Yorkshire Crossbred Pig Population

The number of thoracolumbar vertebrae (NTLV) and the number of ribs (NR) are economically important traits in pigs due to their influence on carcass length and meat yield. Although VRTN is an established key gene, it fails to fully account for population-level variation in vertebral count, necessitating a further exploration of its genetic mechanisms. Given the efficacy of crossbred populations in mapping the genetic determinants of phenotypic variation, we analyzed 439 pigs from a Landrace × Yorkshire cross. Genotyping was performed via a 50 K SNP chip. Both NTLV and NR showed high heritability (0.700 and 0.752, respectively), while the number of lumbar vertebrae (NLV) showed limited variation (92.5% of pigs had NLV = 6). Using the BLINK model, four significant loci were identified. The most significant SNP, rs3469762345, located in the intergenic region between ABCD4 and VRTN, corresponds to a previously known QTL. Additionally, three novel variant sites (rs81211244, rs81347323, and rs81416674) were identified within or near the ALDH7A1, PTPRT, and PAK1 genes, which are known to play a role in bone development. This study uncovers novel swine candidate genes associated with vertebral and rib number variation, subsequently facilitating targeted research into their molecular mechanisms.