Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population

Kejun Wang; Dewu Liu; Jules Hernandez-Sanchez; Jie Chen; Chengkun Liu; Zhenfang Wu; Meiying Fang; Ning Li

doi:10.1371/journal.pone.0139207

Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population

PLoS One. 2015 Sep 29;10(9):e0139207. doi: 10.1371/journal.pone.0139207. eCollection 2015.

Authors

Kejun Wang¹, Dewu Liu², Jules Hernandez-Sanchez³, Jie Chen¹, Chengkun Liu¹, Zhenfang Wu², Meiying Fang¹, Ning Li⁴

Affiliations

¹ Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
² Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
³ Research Methods Group| Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology (QUT), 60 Musk Ave/cnr. Blamey St, Kelvin Grove, QLD 4059, Australia.
⁴ State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100094, People's Republic of China.

Abstract

In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1), seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3), and one for average daily gain (COL27A1). Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

Publication types

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

MeSH terms

Animals
Genome-Wide Association Study
Haplotypes
Male
Meat / analysis*
Meat-Packing Industry
Phenotype
Polymorphism, Single Nucleotide / genetics
Principal Component Analysis
Quantitative Trait Loci / genetics
Sus scrofa / genetics*
Sus scrofa / growth & development*

Grants and funding

This work was supported by the National High Technology and Science Development Plan of China (2011AA100302), Natural Science Foundation of China (NSFC, Grant 31072002, 31372275), State Major Basic Research Development Program of China 973 Project (2014CB138504), Program for New Century Excellent Talents in University (NCET-11-0480), and Program for Changjiang Scholar and Innovation Research Team in University (IRT1191).