Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

Huiyu Wang; Xiaoyi Wang; Mingli Li; Hao Sun; Qiang Chen; Dawei Yan; Xinxing Dong; Yuchun Pan; Shaoxiong Lu

doi:10.3390/genes13111990

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

Genes (Basel). 2022 Oct 31;13(11):1990. doi: 10.3390/genes13111990.

Authors

Huiyu Wang^{1

2}, Xiaoyi Wang¹, Mingli Li¹, Hao Sun³, Qiang Chen¹, Dawei Yan¹, Xinxing Dong¹, Yuchun Pan⁴, Shaoxiong Lu¹

Affiliations

¹ Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
² Faculty of Animal Science, Xichang University, Xichang 615000, China.
³ Faculty of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
⁴ Faculty of Animal Science, Zhejiang University, Hangzhou 310058, China.

Abstract

Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30-60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.

Keywords: SLAF-seq; SNPs; genes; genome-wide association study; growth traits; pigs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genome-Wide Association Study*
Phenotype
Polymorphism, Single Nucleotide / genetics
Quantitative Trait Loci* / genetics
Swine / genetics

Grants and funding

This research was supported by the National Natural Science Foundation of China (U1402266), Yunnan Swine Industry Technology System Program (2020KJTX0016), and Yunnan Province Important National Science & Technology Specific Projects (202102AE090039).