Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait
Haonan Zeng,
Zhanming Zhong,
Zhiting Xu,
Jinyan Teng,
Chen Wei,
Zitao Chen,
Wenjing Zhang,
Xiangdong Ding,
Jiaqi Li,
Zhe Zhang
Affiliations
Haonan Zeng
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Zhanming Zhong
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Zhiting Xu
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Jinyan Teng
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Chen Wei
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Zitao Chen
Department of Animal Science, College of Animal Science, Zhejiang University
Wenjing Zhang
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Xiangdong Ding
Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Jiaqi Li
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Zhe Zhang
Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University
Abstract Background Average backfat thickness (BFT) is a critical complex trait in pig and an important indicator for fat deposition and lean rate. Usually, genome-wide association study (GWAS) was used to discover quantitative trait loci (QTLs) of BFT in a single population. However, the power of GWAS is limited by sample size in a single population. Alternatively, meta-analysis of GWAS (metaGWAS) is an attractive method to increase the statistical power by integrating data from multiple breeds and populations. The aim of this study is to identify shared genetic characterization of BFT across breeds in pigs via metaGWAS. Results In this study, we performed metaGWAS on BFT using 15,353 pigs (5,143 Duroc, 7,275 Yorkshire, and 2,935 Landrace) from 19 populations. We detected 40 genome-wide significant SNPs (Bonferroni corrected P < 0.05) and defined five breed-shared QTLs in across-breed metaGWAS. Markers within the five QTL regions explained 7 ~ 9% additive genetic variance and showed strong heritability enrichment. Furthermore, by integrating information from multiple bioinformatics databases, we annotated 46 candidate genes located in the five QTLs. Among them, three important (MC4R, PPARD, and SLC27A1) and seven suggestive candidate genes (PHLPP1, NUDT3, ILRUN, RELCH, KCNQ5, ITPR3, and U3) were identified. Conclusion QTLs and candidate genes underlying BFT across breeds were identified via metaGWAS from multiple populations. Our findings contribute to the understanding of the genetic architecture of BFT and the regulating mechanism underlying fat deposition in pigs.
