Genome-wide Association Study And Analysis Of Candidate Genes Of The Number Of Thoracic Vertebrae In Pig

The spine is the backbone of the mammalian body which has high heritability.The variation of the number of vertebrae mainly refers to the variation of the number of thoracolumbar vertebrae.The number of thoracic vertabrae is equal to ribs number.The number of the somites and the attribute pattern of the spine affect the vertebrae.In order to identify the major quantitative trait locus(QTL)and important candidate genes affecting the number of thoracic vertabrae,we collected the ear tissues of 542 individuals in the Large White × Minzhu intercross pig population and 1104 individuals in Beijing Black Pig,and then genotyping these individuals using the Porcine SNP60 and SNP50 Genotyping Beadchip.For genome-wide association analysis(GWAS),using the mixed linear model in the TASSEL software.In the Large White × Minzhu intercross pig population,all the animals were genotyped for 37 missense or splice variants in a previously reported 951-kb interval on SSC7 and 147 SNPs(single nucleotide polymorphisms)on SSC14.First,we conducted a GWAS for the number of thoracic vertebrae with the vertebrae as a covariate to identify the most significant SNP related to the number of thoracic vertebrae.The result indicated that there are 31 SNPs on SSC7 affecting the thoracic vertebrae.Further linkage disequilibrium analysis showed that there is a QTL in the 479 Kb region on SSC7,which contains the FOS gene,an important candidate gene for the number of pig thoracic vertebrae.A conditional GWAS was performed by fixing the strongest significant SNP,M1GA0010658,on SSC7.There were two SNPs located in BMPR1 A were found to have significant genome-wide association.The leading SNP was S14＿87859370,which accounted for 3.86% of the phenotypic variance.The influence of S14＿87859370 locus on the number of thoracic vertebrae was further identified in Songliao Black Pig and Large White Pig population,and the BMPR1 A gene was finally determined as a causative gene and S14＿87859370 in this gene has a significant effect on the number of thoracic vertebrae in Songliao Black Pig population.In the Beijing Black Pig population,14 SNPs affecting the thoracic vertebrae were defined within a2.29 Mb on SSC7.The most significantly associated SNP was Affx-114687136(P=2.6734E-29).The QTL region affecting the number of thoracic vertebrae on SSC7 covered the previously reported VRTN and LTBP2 candidate genes.A QTL confidence interval of 221 kb was determined by haplotype analysis,and 5 genes containing important SNPs were identified based on the annotation of the pig reference genome.4 SNPs were identified on SSC6.The most significantly associated SNP was WU＿10.2＿6＿98948339(P=1.06E-07).Further analysis indicated that VSX2,GREB1 L and MIB1 were candidate genes related to the variation of the number of pig thoracic vertebrae.In this study,the FOS and VSX2 genes on SSC7,the GREB1 L and MIB1 on SSC6,and the BMPR1 A gene on SSC14 were identified as the important candidate genes that affecting the variation of the number of thoracic vertebrae through GWAS and fine mapping methods.This study shows that the number of thoracic vertebrae is a complex trait controlled by multiple genes,which can enrich the molecular theory of the regulation mechanism of the number of thoracic vertebrae in pigs,and provide molecular markers for the selection and improvement of the rib number of pig.