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Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait

文献类型： 外文期刊

作者： Zeng, Haonan 1 ; Zhong, Zhanming 1 ; Xu, Zhiting 1 ; Teng, Jinyan 1 ; Wei, Chen 1 ; Chen, Zitao 2 ; Zhang, Wenjing 1 ; Ding, Xiangdong 3 ; Li, Jiaqi 1 ; Zhang, Zhe 1 ;

作者机构： 1.South China Agr Univ, Coll Anim Sci, Natl Engn Res Ctr Breeding Swine Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou 510642, Peoples R China

2.Zhejiang Univ, Coll Anim Sci, Dept Anim Sci, Hangzhou 310058, Peoples R China

3.China Agr Univ, Coll Anim Sci & Technol, Natl Engn Lab Anim Breeding, Minist Agr & Rural Affairs,Key Lab Anim Genet & B, Beijing 100193, Peoples R China

关键词： Pig; GWAS; meta-analysis; Backfat thickness; QTL

期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCI

摘要： 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 (PHLPPI, 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.

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