Premium
Unravelling the genetic loci for growth and carcass traits in Chinese Bamaxiang pigs based on a 1.4 million SNP array
Author(s) -
Gong Huanfa,
Xiao Shijun,
Li Wanbo,
Huang Tao,
Huang Xiaochang,
Yan Guorong,
Huang Yizhong,
Qiu Hengqing,
Jiang Kai,
Wang Xiaopeng,
Zhang Hui,
Tang Jianhong,
Li Lin,
Li Yiping,
Wang Chenbin,
Qiao Chuanmin,
Ren Jun,
Huang Lusheng,
Yang Bin
Publication year - 2019
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12365
Subject(s) - biology , genome wide association study , snp , genetics , genetic architecture , heritability , breed , quantitative trait locus , purebred , genetic association , single nucleotide polymorphism , genotype , gene
Bamaxiang pig is from Guangxi province in China, characterized by its small body size and two‐end black coat colour. It is an important indigenous breed for local pork market and excellent animal model for biomedical research. In this study, we performed genomewide association studies (GWAS) on 43 growth and carcass traits in 315 purebred Bamaxiang pigs based on a 1.4 million SNP array. We observed considerable phenotypic variability in the growth and carcass traits in the Bamaxiang pigs. The corresponding SNP based heritability varied greatly across the 43 traits and ranged from 9.0% to 88%. Through a conditional GWAS, we identified 53 significant associations for 35 traits at p value threshold of 10 −6 . Among which, 26 associations on chromosome 3, 7, 14 and X passed a genomewide significance threshold of 5 × 10 −8 . The most remarkable loci were at around 30.6 Mb on chromosome 7, which had growth stage‐dependent effects on body lengths and cannon circumferences and showed large effects on multiple carcass traits. We discussed HMGA1 NUDT3 , EIF2AK1, TMEM132C and AFF2 that near the lead SNP of significant loci as plausible candidate genes for corresponding traits. We also showed that including phenotypic covariate in GWAS can help to reveal additional significant loci for the target traits. The results provide insight into the genetic architecture of growth and carcass traits in Bamaxiang pigs.