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Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population

As one of the main breeding selection criteria, external appearance has special economic importance in the hog industry. In this study, an Illumina Porcine SNP60 BeadChip was used to conduct a genome-wide association study (GWAS) in 605 pigs of the F(2) generation derived from a Large White × Minzhu...

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Autores principales: Wang, Ligang, Zhang, Longchao, Yan, Hua, Liu, Xin, Li, Na, Liang, Jing, Pu, Lei, Zhang, Yuebo, Shi, Huibi, Zhao, Kebin, Wang, Lixian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121205/
https://www.ncbi.nlm.nih.gov/pubmed/25090094
http://dx.doi.org/10.1371/journal.pone.0103766
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author Wang, Ligang
Zhang, Longchao
Yan, Hua
Liu, Xin
Li, Na
Liang, Jing
Pu, Lei
Zhang, Yuebo
Shi, Huibi
Zhao, Kebin
Wang, Lixian
author_facet Wang, Ligang
Zhang, Longchao
Yan, Hua
Liu, Xin
Li, Na
Liang, Jing
Pu, Lei
Zhang, Yuebo
Shi, Huibi
Zhao, Kebin
Wang, Lixian
author_sort Wang, Ligang
collection PubMed
description As one of the main breeding selection criteria, external appearance has special economic importance in the hog industry. In this study, an Illumina Porcine SNP60 BeadChip was used to conduct a genome-wide association study (GWAS) in 605 pigs of the F(2) generation derived from a Large White × Minzhu intercross. Traits under study were abdominal circumference (AC), body height (BH), body length (BL), cannon bone circumference (CBC), chest depth (CD), chest width (CW), rump circumference (RC), rump width (RW), scapula width (SW), and waist width (WW). A total of 138 SNPs (the most significant being MARC0033464) on chromosome 7 were found to be associated with BH, BL, CBC, and RC (P-value  = 4.15E-6). One SNP on chromosome 1 was found to be associated with CD at genome-wide significance levels. The percentage phenotypic variance of these significant SNPs ranged from 0.1–25.48%. Moreover, a conditional analysis revealed that the significant SNPs were derived from a single quantitative trait locus (QTL) and indicated additional chromosome-wide significant association for 25 SNPs on SSC4 (BL, CBC) and 9 SNPs on SSC7 (RC). Linkage analysis revealed two complete linkage disequilibrium haplotype blocks that contained seven and four SNPs, respectively. In block 1, the most significant SNP, MARC0033464, was present. Annotations from pig reference genome suggested six genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in block 1 (495 kb), and one gene (SCUBE3) in block 3 (124 kb). Functional analysis indicated that HMGA1 and SCUBE3 genes are the potential genes controlling BH, BL, and RC in pigs, with an application in breeding programs. We screened several candidate intervals and genes based on SNP location and gene function, and predicted their function using bioinformatics analyses.
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spelling pubmed-41212052014-08-05 Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population Wang, Ligang Zhang, Longchao Yan, Hua Liu, Xin Li, Na Liang, Jing Pu, Lei Zhang, Yuebo Shi, Huibi Zhao, Kebin Wang, Lixian PLoS One Research Article As one of the main breeding selection criteria, external appearance has special economic importance in the hog industry. In this study, an Illumina Porcine SNP60 BeadChip was used to conduct a genome-wide association study (GWAS) in 605 pigs of the F(2) generation derived from a Large White × Minzhu intercross. Traits under study were abdominal circumference (AC), body height (BH), body length (BL), cannon bone circumference (CBC), chest depth (CD), chest width (CW), rump circumference (RC), rump width (RW), scapula width (SW), and waist width (WW). A total of 138 SNPs (the most significant being MARC0033464) on chromosome 7 were found to be associated with BH, BL, CBC, and RC (P-value  = 4.15E-6). One SNP on chromosome 1 was found to be associated with CD at genome-wide significance levels. The percentage phenotypic variance of these significant SNPs ranged from 0.1–25.48%. Moreover, a conditional analysis revealed that the significant SNPs were derived from a single quantitative trait locus (QTL) and indicated additional chromosome-wide significant association for 25 SNPs on SSC4 (BL, CBC) and 9 SNPs on SSC7 (RC). Linkage analysis revealed two complete linkage disequilibrium haplotype blocks that contained seven and four SNPs, respectively. In block 1, the most significant SNP, MARC0033464, was present. Annotations from pig reference genome suggested six genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in block 1 (495 kb), and one gene (SCUBE3) in block 3 (124 kb). Functional analysis indicated that HMGA1 and SCUBE3 genes are the potential genes controlling BH, BL, and RC in pigs, with an application in breeding programs. We screened several candidate intervals and genes based on SNP location and gene function, and predicted their function using bioinformatics analyses. Public Library of Science 2014-08-04 /pmc/articles/PMC4121205/ /pubmed/25090094 http://dx.doi.org/10.1371/journal.pone.0103766 Text en © 2014 Wang 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
Wang, Ligang
Zhang, Longchao
Yan, Hua
Liu, Xin
Li, Na
Liang, Jing
Pu, Lei
Zhang, Yuebo
Shi, Huibi
Zhao, Kebin
Wang, Lixian
Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population
title Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population
title_full Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population
title_fullStr Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population
title_full_unstemmed Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population
title_short Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population
title_sort genome-wide association studies identify the loci for 5 exterior traits in a large white × minzhu pig population
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121205/
https://www.ncbi.nlm.nih.gov/pubmed/25090094
http://dx.doi.org/10.1371/journal.pone.0103766
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