SONG Xing-chao, WANG Sha-sha, WANG Yun-yan, MEI Jie, LIANG Zheng-qi, BA Jia-wen. 2025: Cloning,bioinformatics and sequence variation analysis of MC1R gene in Danio rerio. Journal of Southern Agriculture, 56(7): 2317-2327. DOI: 10.3969/j.issn.2095-1191.2025.07.025
Citation: SONG Xing-chao, WANG Sha-sha, WANG Yun-yan, MEI Jie, LIANG Zheng-qi, BA Jia-wen. 2025: Cloning,bioinformatics and sequence variation analysis of MC1R gene in Danio rerio. Journal of Southern Agriculture, 56(7): 2317-2327. DOI: 10.3969/j.issn.2095-1191.2025.07.025

Cloning,bioinformatics and sequence variation analysis of MC1R gene in Danio rerio

  • Objective This study aimed to clone and identify the coding sequence (CDS) of the melanocortin-1 receptor (MC1R) gene in zebrafish (Danio rerio), and to conduct bioinformatics and sequence variation analysis, so as to provide fundamental materials for elucidating the biological function of the MC1R gene and the regulation mechanisms of zebrafish body color traits.Method Using muscle tissue DNA from 219 samples of red, yellow, and blue zebrafish populations as templates, CDS sequences of the MC1R gene of zebrafish were obtained through PCR amplification, clo-ning, sequencing, and assembly to perform bioinformatics analysis and gene sequence variation analysis.Result The full-length of MC1R gene was 1404 bp, with a CDS of 972 bp, encoding 323 amino acid residues. The MC1R protein contained seven transmembrane domains, four extracellular regions, and four intracellular regions, exhibiting a typical cell surface receptor-like structure. The protein was mainly localized to the plasma membrane and possessed four potential N-glycosylation sites and 26 phosphorylation sites. The zebrafish MC1R gene showed high similarity to that of Megalobrama amblycephala and Anabarilius grahami, demonstrating the nearest genetic distance and close genetic relationships. Two variant sites were identified in red, yellow, and blue zebrafish populations: one variant site (g.334T>C) was located in the CDS and exhibited both TT and TC genotypes, without causing any change in amino acid; the other variant site was located in the 3'-untranslated region (3'-UTR) (g.276A>T) and exhibited both AA and AT genotypes. The frequencies of the two variants, g.334T>C and g.276A>T, were consistent across color groups.Conclusion The MC1R gene sequence is conserved and somewhat diverse across fish species, suggesting that the protein structure is relatively conserved and functionally similar across species. The MC1R gene can be used as an effective molecular marker for studying the evolutionary relationships of different fish systems. It is relatively conserved in red, yellow, and blue zebrafish populations, and contains two variant sites (g.276A>T and g.334T>C) which may be in linkage.
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