Integrated Single-Trait and Multi-Trait GWASs Reveal the Genetic Architecture of Internal Organ Weight in Pigs
by
, ,
Xuehua Li
1,†,
Jie Wu
1,†,
Zhanwei Zhuang
1,
Yong Ye
1,
Shenping Zhou
1,
Yibin Qiu
1,
Donglin Ruan
1,
Shiyuan Wang
1,
Jie Yang
1,2,
Zhenfang Wu
1,2,3,
Gengyuan Cai
1,2,* and
Enqin Zheng
1,2,* 1
College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
2
Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
3
Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Animals 2023, 13(5), 808; https://doi.org/10.3390/ani13050808
Submission received: 7 January 2023
/
Revised: 18 February 2023
/
Accepted: 20 February 2023
/
Published: 23 February 2023
(This article belongs to the Section Pigs)
Simple Summary
In this study, bioinformatics approaches were used to better understand the genetic architecture of internal organ weights in three-way crossbred commercial pigs and to map genetic markers and genes. For this purpose, we used single-trait and multi-trait genome-wide association studies (GWASs) followed by a haplotype block analysis. We explored the key genetic markers and genes from the internal organ weight genome-wide association study results of three-way crossbred commercial pigs. In this manner, five genes, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, were defined as central in affecting internal organ weight in pigs. Moreover, APK1, ANO6, and UNC5C were identified to be pleiotropic in multi-trait GWASs. These results can be applied to various types of genomic studies of pigs.
Abstract
Internal organ weight is an essential indicator of growth status as it reflects the level of growth and development in pigs. However, the associated genetic architecture has not been well explored because phenotypes are difficult to obtain. Herein, we performed single-trait and multi-trait genome-wide association studies (GWASs) to map the genetic markers and genes associated with six internal organ weight traits (including heart weight, liver weight, spleen weight, lung weight, kidney weight, and stomach weight) in 1518 three-way crossbred commercial pigs. In summation, single-trait GWASs identified a total of 24 significant single- nucleotide polymorphisms (SNPs) and 5 promising candidate genes, namely, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, as being associated with the six internal organ weight traits analyzed. Multi-trait GWAS identified four SNPs with polymorphisms localized on the APK1, ANO6, and UNC5C genes and improved the statistical efficacy of single-trait GWASs. Furthermore, our study was the first to use GWASs to identify SNPs associated with stomach weight in pigs. In conclusion, our exploration of the genetic architecture of internal organ weights helps us better understand growth traits, and the key SNPs identified could play a potential role in animal breeding programs.
Keywords:
internal organ weight; GWAS; DLY pigs; genetic architecture
