Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population

Ligang Wang; Longchao Zhang; Hua Yan; Xin Liu; Na Li; Jing Liang; Lei Pu; Yuebo Zhang; Huibi Shi; Kebin Zhao; Lixian Wang

doi:10.1371/journal.pone.0103766

Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population

PLoS One. 2014 Aug 4;9(8):e103766. doi: 10.1371/journal.pone.0103766. eCollection 2014.

Authors

Ligang Wang¹, Longchao Zhang¹, Hua Yan¹, Xin Liu¹, Na Li², Jing Liang¹, Lei Pu¹, Yuebo Zhang¹, Huibi Shi¹, Kebin Zhao¹, Lixian Wang¹

Affiliations

¹ Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
² Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China; Jilin Academy of Agricultural Sciences, Changchun, China.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Body Height / genetics
Computational Biology
Crosses, Genetic*
Female
Genome-Wide Association Study*
Haplotypes / genetics
Humans
Linkage Disequilibrium / genetics
Male
Phenotype
Polymorphism, Single Nucleotide / genetics
Quantitative Trait Loci / genetics*
Quantitative Trait, Heritable
Sus scrofa / anatomy & histology
Sus scrofa / genetics*

Grants and funding

This research was supported by The Agricultural Science and Technology Innovation Program (ASTIP-IAS02), National Key Technology R&D Program of China (No. 2011BAD28B01), National Natural Science Foundation of China (31201781), earmarked fund for Modern Agro-industry Technology Research System, National Technology Program of China (No. 2011ZX08006-003) and Chinese Academy of Agricultural Sciences Foundation (No. 2014ZL006, 2011cj-5, No. 2012ZL069 and 2014ywf-yb-8). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.