title: A further look at porcine chromosome 7 reveals VRTN variants associated with vertebral number in Chinese and Western pigs.
abstract: 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.
authors: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People's Republic of China.
authors: Yin
authors: Y
authors: Fan
authors: Yuyun
authors: Y
authors: Xing
authors: Zhiyan
authors: Z
authors: Zhang
authors: Huashui
authors: H
authors: Ai
authors: Zixuan
authors: Z
authors: Ouyang
authors: Jing
authors: J
authors: Ouyang
authors: Ming
authors: M
authors: Yang
authors: Pinghua
authors: P
authors: Li
authors: Yijie
authors: Y
authors: Chen
authors: Jun
authors: J
authors: Gao
authors: Lin
authors: L
authors: Li
authors: Lusheng
authors: L
authors: Huang
authors: Jun
authors: J
authors: Ren
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D033481:Chromosomes, Mammalian; D023061:Gene Order; D056726:Genetic Association Studies; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D009154:Mutation; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D013552:Swine; D013904:Thoracic Vertebrae / Q000033:anatomy & histology*
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