Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

BMC Genomics

Shenping Zhou¹  Qian Geng¹  Sixiu Huang¹  Yong Ye¹  Zhanwei Zhuang¹  Jie Wu¹  Yibin Qiu¹  Rongrong Ding²  Gengyuan Cai³  Zhenfang Wu³  Zheng Xu⁴  Jie Yang⁴  Ming Yang⁵ 

[1] College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, 510642, Guangzhou, Guangdong, People’s Republic of China;College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, 510642, Guangzhou, Guangdong, People’s Republic of China;Guangdong Wens Breeding Swine Technology Co., Ltd., 527400, Yunfu, Guangdong, People’s Republic of China;College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, 510642, Guangzhou, Guangdong, People’s Republic of China;Guangdong Wens Breeding Swine Technology Co., Ltd., 527400, Yunfu, Guangdong, People’s Republic of China;Lingnan Guangdong Laboratory of Modern Agriculture, 510642, Guangzhou, People’s Republic of China;College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, 510642, Guangzhou, Guangdong, People’s Republic of China;Lingnan Guangdong Laboratory of Modern Agriculture, 510642, Guangzhou, People’s Republic of China;Guangdong Wens Breeding Swine Technology Co., Ltd., 527400, Yunfu, Guangdong, People’s Republic of China;

关键词: Copy number variation;    CNVR-based GWAS;    Growth;    Fatness;    Duroc pigs;   

DOI  :  10.1186/s12864-021-07654-7

来源: Springer

【 摘 要 】

BackgroundIn the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. Copy number variation (CNV), an important source of genetic diversity, can affect a variety of complex traits and diseases and has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs using SNP genotyping data from 6627 animals. We also performed a copy number variation region (CNVR)-based genome-wide association studies (GWAS) for growth and fatness traits in two Duroc populations.ResultsOur study identified 953 nonredundant CNVRs in U.S. and Canadian Duroc pigs, covering 246.89 Mb (~ 10.90%) of the pig autosomal genome. Of these, 802 CNVRs were in U.S. Duroc pigs with 499 CNVRs were in Canadian Duroc pigs, indicating 348 CNVRs were shared by the two populations. Experimentally, 77.8% of nine randomly selected CNVRs were validated through quantitative PCR (qPCR). We also identified 35 CNVRs with significant association with growth and fatness traits using CNVR-based GWAS. Ten of these CNVRs were associated with both ADG and AGE traits in U.S. Duroc pigs. Notably, four CNVRs showed significant associations with ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. In Canadian Duroc pigs, nine CNVRs were significantly associated with both ADG and AGE traits. Further bioinformatic analysis identified a subset of potential candidate genes, including PDGFA, GPER1, PNPLA2 and BSCL2.ConclusionsThe present study provides a necessary supplement to the CNV map of the Duroc genome through large-scale population genotyping. In addition, the CNVR-based GWAS results provide a meaningful way to elucidate the genetic mechanisms underlying complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in the molecular-guided breeding of modern commercial pigs.

【 授权许可】

CC BY