Genome-Wide Association Study and FST Analysis Reveal Four Quantitative Trait Loci and Six Candidate Genes for Meat Color in Pigs

Hang Liu; Liming Hou; Wuduo Zhou; Binbin Wang; Pingping Han; Chen Gao; Peipei Niu; Zongping Zhang; Qiang Li; Ruihua Huang; Pinghua Li

doi:10.3389/fgene.2022.768710

Genome-Wide Association Study and F_ST Analysis Reveal Four Quantitative Trait Loci and Six Candidate Genes for Meat Color in Pigs

Front Genet. 2022 Apr 8:13:768710. doi: 10.3389/fgene.2022.768710. eCollection 2022.

Authors

Hang Liu^{1

2

3}, Liming Hou^{1

2}, Wuduo Zhou¹, Binbin Wang^{1

2}, Pingping Han¹, Chen Gao^{1

2}, Peipei Niu², Zongping Zhang², Qiang Li⁴, Ruihua Huang^{1

2}, Pinghua Li^{1

2}

Affiliations

¹ Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.
² Huaian Academy, Nanjing Agricultural University, Huaian, China.
³ Hangzhou Academy of Agricultural Sciences, Hangzhou, China.
⁴ Huaiyin Pig Breeding Farm of Huaian City, Huaian, China.

Abstract

Meat color is the primary criterion by which consumers evaluate meat quality. However, there are a few candidate genes and molecular markers of meat color that were reported for pig molecular breeding. The purpose of the present study is to identify the candidate genes affecting meat color and provide the theoretical basis for meat color molecular breeding. A total of 306 Suhuai pigs were slaughtered, and meat color was evaluated at 45 min and 24 h after slaughter by CIELAB color space. All individuals were genotyped using GeneSeek GGP-Porcine 80K SNP BeadChip. The genomic estimated breeding values (GEBVs), heritability, and genetic correlation of meat color were calculated by DMU software. The genome-wide association studies (GWASs) and the fixation index (F_ST) tests were performed to identify SNPs related to meat color, and the candidate genes within 1 Mb upstream and downstream of significant SNPs were screened by functional enrichment analysis. The heritability of L* 45 min, L* 24 h, a* 45 min, a* 24 h, b* 45 min, and b* 24 h was 0.20, 0.16, 0.30, 0.13, 0.29, and 0.22, respectively. The genetic correlation between a* (a* 45 min and a* 24 h) and L* (L* 45 min and L* 24 h) is strong, whereas the genetic correlation between b* 45 min and b* 24 h is weak. Forty-nine significant SNPs associated with meat color were identified through GWAS and F_ST tests. Among these SNPs, 34 SNPs were associated with L* 45 min within a 5-Mb region on Sus scrofa chromosome 11 (SSC11); 22 SNPs were associated with a* 45 min within a 14.72-Mb region on SSC16; six SNPs were associated with b* 45 min within a 4.22-Mb region on SSC13; 11 SNPs were associated with b* 24 h within a 2.12-Mb region on SSC3. These regions did not overlap with meat color-associated QTLs reported previously. Moreover, six candidate genes (HOMER1, PIK3CG, PIK3CA, VCAN, FABP3, and FKBP1B), functionally related to muscle development, phosphatidylinositol phosphorylation, and lipid binding, were detected around these significant SNPs. Taken together, our results provide a set of potential molecular markers for the genetic improvement of meat color in pigs.

Keywords: GWAS; candidate genes; heritability; marker; meat color; pigs.