Analysis of VRTN, NR6A1 and LTBP2 gene polymorphisms in Lijiang pigs and their association with the number of thoracic vertebrae

To explore the polymorphisms of the VRTN, NR6A1, and LTBP2 genes and their association with thoracic vertebrae count in Lijiang pigs, genotyping these genes’ exons and the VRTN promoter region was conducted in 205 individuals. Polymerase chain reaction (PCR) and Sanger sequencing were used for this purpose. Genotype and allele frequencies of the identified variants were calculated, and their associations with thoracic vertebrae count were analyzed. A total of eight missense mutations and one insertion mutation were identified. Moderate polymorphism was detected in VRTN (g.97622607G>A, g.97623006G>A, g.97623046C>T), NR6A1 (g.265347265T>C), and LTBP2 (SSC7:97765472C>G), while VRTN (g.976158896_976158897ins291) and LTBP2 (SSC7:97770379T>C) showed low polymorphism. Importantly, the VRTN variant g.976158896_976158897ins291 and the LTBP2 variant SSC7:97770379T>C were significantly associated with thoracic vertebrae count (P<0.01). Further, the NR6A1 variant g.265347265T>C was also significantly associated with thoracic vertebrae count (P<0.05). The variants g.976158896_976158897ins291 of VRTN, g.265347265T>C of NR6A1, andSSC7:97770379T>C of LTBP2 significantly influence the number of thoracic vertebrae, providing valuable insights for the molecular breeding of Lijiang pigs concerning this trait.