Cargando…

A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs

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 herei...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634791/
https://www.ncbi.nlm.nih.gov/pubmed/23638110
http://dx.doi.org/10.1371/journal.pone.0062534
_version_ 1782267152692150272
author 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
author_facet 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
author_sort Fan, Yin
collection PubMed
description 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.
format Online
Article
Text
id pubmed-3634791
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-36347912013-05-01 A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs 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 PLoS One Research Article 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. Public Library of Science 2013-04-24 /pmc/articles/PMC3634791/ /pubmed/23638110 http://dx.doi.org/10.1371/journal.pone.0062534 Text en © 2013 Fan et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
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
A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs
title A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs
title_full A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs
title_fullStr A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs
title_full_unstemmed A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs
title_short A Further Look at Porcine Chromosome 7 Reveals VRTN Variants Associated with Vertebral Number in Chinese and Western Pigs
title_sort further look at porcine chromosome 7 reveals vrtn variants associated with vertebral number in chinese and western pigs
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634791/
https://www.ncbi.nlm.nih.gov/pubmed/23638110
http://dx.doi.org/10.1371/journal.pone.0062534
work_keys_str_mv AT fanyin afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT xingyuyun afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT zhangzhiyan afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT aihuashui afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT ouyangzixuan afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT ouyangjing afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT yangming afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT lipinghua afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT chenyijie afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT gaojun afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT lilin afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT huanglusheng afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT renjun afurtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT fanyin furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT xingyuyun furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT zhangzhiyan furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT aihuashui furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT ouyangzixuan furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT ouyangjing furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT yangming furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT lipinghua furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT chenyijie furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT gaojun furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT lilin furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT huanglusheng furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs
AT renjun furtherlookatporcinechromosome7revealsvrtnvariantsassociatedwithvertebralnumberinchineseandwesternpigs