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Liu C, Chen Z, Zhang Z, Wang Z, Guo X, Pan Y, Wang Q. Unveiling the Genetic Mechanism of Meat Color in Pigs through GWAS, Multi-Tissue, and Single-Cell Transcriptome Signatures Exploration. Int J Mol Sci 2024; 25:3682. [PMID: 38612491 PMCID: PMC11012088 DOI: 10.3390/ijms25073682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
Meat color traits directly influence consumer acceptability and purchasing decisions. Nevertheless, there is a paucity of comprehensive investigation into the genetic mechanisms underlying meat color traits in pigs. Utilizing genome-wide association studies (GWAS) on five meat color traits and the detection of selection signatures in pig breeds exhibiting distinct meat color characteristics, we identified a promising candidate SNP, 6_69103754, exhibiting varying allele frequencies among pigs with different meat color characteristics. This SNP has the potential to affect the redness and chroma index values of pork. Moreover, transcriptome-wide association studies (TWAS) analysis revealed the expression of candidate genes associated with meat color traits in specific tissues. Notably, the largest number of candidate genes were observed from transcripts derived from adipose, liver, lung, spleen tissues, and macrophage cell type, indicating their crucial role in meat color development. Several shared genes associated with redness, yellowness, and chroma indices traits were identified, including RINL in adipose tissue, ENSSSCG00000034844 and ITIH1 in liver tissue, TPX2 and MFAP2 in lung tissue, and ZBTB17, FAM131C, KIFC3, NTPCR, and ENGSSSCG00000045605 in spleen tissue. Furthermore, single-cell enrichment analysis revealed a significant association between the immune system and meat color. This finding underscores the significance of the immune system associated with meat color. Overall, our study provides a comprehensive analysis of the genetic mechanisms underlying meat color traits, offering valuable insights for future breeding efforts aimed at improving meat quality.
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Affiliation(s)
- Cheng Liu
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou 310058, China; (C.L.); (Z.C.); (Z.Z.); (Z.W.); (X.G.); (Y.P.)
| | - Zitao Chen
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou 310058, China; (C.L.); (Z.C.); (Z.Z.); (Z.W.); (X.G.); (Y.P.)
| | - Zhe Zhang
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou 310058, China; (C.L.); (Z.C.); (Z.Z.); (Z.W.); (X.G.); (Y.P.)
| | - Zhen Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou 310058, China; (C.L.); (Z.C.); (Z.Z.); (Z.W.); (X.G.); (Y.P.)
| | - Xiaoling Guo
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou 310058, China; (C.L.); (Z.C.); (Z.Z.); (Z.W.); (X.G.); (Y.P.)
| | - Yuchun Pan
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou 310058, China; (C.L.); (Z.C.); (Z.Z.); (Z.W.); (X.G.); (Y.P.)
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
| | - Qishan Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou 310058, China; (C.L.); (Z.C.); (Z.Z.); (Z.W.); (X.G.); (Y.P.)
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
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