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 F2 generation derived from a Large White × Minzhu i...

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Autores principales:	Ligang Wang, Longchao Zhang, Hua Yan, Xin Liu, Na Li, Jing Liang, Lei Pu, Yuebo Zhang, Huibi Shi, Kebin Zhao, Lixian Wang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7d0e80975c5c416bb92fe7471afa1cc3
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spelling	oai:doaj.org-article:7d0e80975c5c416bb92fe7471afa1cc32021-11-25T06:06:11ZGenome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population.1932-620310.1371/journal.pone.0103766https://doaj.org/article/7d0e80975c5c416bb92fe7471afa1cc32014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25090094/?tool=EBIhttps://doaj.org/toc/1932-6203As 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 F2 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.Ligang WangLongchao ZhangHua YanXin LiuNa LiJing LiangLei PuYuebo ZhangHuibi ShiKebin ZhaoLixian WangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e103766 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ligang Wang Longchao Zhang Hua Yan Xin Liu Na Li Jing Liang Lei Pu Yuebo Zhang Huibi Shi Kebin Zhao Lixian Wang Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population.
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 F2 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.
format	article
author	Ligang Wang Longchao Zhang Hua Yan Xin Liu Na Li Jing Liang Lei Pu Yuebo Zhang Huibi Shi Kebin Zhao Lixian Wang
author_facet	Ligang Wang Longchao Zhang Hua Yan Xin Liu Na Li Jing Liang Lei Pu Yuebo Zhang Huibi Shi Kebin Zhao Lixian Wang
author_sort	Ligang Wang
title	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_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_sort	genome-wide association studies identify the loci for 5 exterior traits in a large white × minzhu pig population.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/7d0e80975c5c416bb92fe7471afa1cc3
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Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population.

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