A further look at porcine chromosome 7 reveals VRTN variants associated with vertebral number in Chinese and Western pigs

• Published in: PloS one 2013-04, Vol.8 (4), p.e62534-e62534
• Main Authors: Fan, Yin, Xing, Yuyun, Zhang, Zhiyan, Ai, Huashui, Ouyang, Zixuan, Ouyang, Jing, Yang, Ming, Li, Pinghua, Chen, Yijie, Gao, Jun, Li, Lin, Huang, Lusheng, Ren, Jun
• Format: Article
• Language: English
• Subjects: Agriculture; Analysis; Animals; Bioinformatics; Biology; Biotechnology; Breeding; Chromosome 7; Chromosome Mapping; Chromosomes, Mammalian; Deoxyribonucleic acid; DNA; DNA chips; DNA microarrays; Domestication; Economic importance; Gene mapping; Gene Order; Genetic aspects; Genetic Association Studies; Genetic Variation; Genetics; Genome-Wide Association Study; Genomes; Genomics; Genotype; Genotypes; Hogs; Indigenous animals; Laboratories; Linkage disequilibrium; Livestock breeding; Mammals; Meat; Meat production; Mutation; Population; Populations; Progeny; Quantitative genetics; Quantitative Trait Loci; Quantitative Trait, Heritable; Spine; Studies; Suidae; Swine; Thoracic Vertebrae - anatomy & histology; Thorax; Vertebra; Vertebrae
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0062534

The number of vertebrae is an economically important trait that affects carcass length and meat production in pigs. A major quantitative trait locus (QTL) for thoracic vertebral number has been repeatedly identified on pig chromosome (SSC) 7. To dissect the genetic basis of the major locus, we herein genotyped a large sample of animals from 3 experimental populations of Chinese and Western origins using 60K DNA chips. Genome-wide association studies consistently identified the locus across the 3 populations and mapped the locus to a 947-Kb region on SSC7. An identical-by-descent sharing assay refined the locus to a 100-Kb segment that harbors only two genes including VRTN and SYNDIG1L. Of them, VRNT has been proposed as a strong candidate of the major locus in Western modern breeds. Further, we resequenced the VRTN gene using DNA samples of 35 parental animals with known QTL genotypes by progeny testing. Concordance tests revealed 4 candidate causal variants as their genotypes showed the perfect segregation with QTL genotypes of the tested animals. An integrative analysis of evolutional constraints and functional elements supported two VRTN variants in a complete linkage disequilibrium phase as the most likely causal mutations. The promising variants significantly affect the number of thoracic vertebrae (one vertebra) in large scale outbred animals, and are segregating at rather high frequencies in Western pigs and at relatively low frequencies in a number of Chinese breeds. Altogether, we show that VRTN variants are significantly associated with the number of thoracic vertebrae in both Chinese and Western pigs. The finding advances our understanding of the genetic architecture of the vertebral number in pigs. Furthermore, our finding is of economical importance as it provides a robust breeding tool for the improvement of vertebral number and meat production in both Chinese indigenous pigs and Western present-day commercial pigs.