Genetic fine-mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism

文献类型： 外文期刊

第一作者： Liu, Hehe

作者： Liu, Hehe;Xi, Yang;Tang, Qian;Qi, Jingjing;Liu, Hehe;Zhou, Zhengkui;Guo, Zhanbao;Fan, Wenlei;Hu, Jian;Xu, Yaxi;Liang, Suyun;Xie, Ming;Tang, Jing;Zhang, Yunsheng;Hou, Shuisheng;Liu, Hehe;Zhou, Zhengkui;Guo, Zhanbao;Fan, Wenlei;Hu, Jian;Xu, Yaxi;Liang, Suyun;Xie, Ming;Tang, Jing;Zhang, Yunsheng;Hou, Shuisheng;Hou, Shuisheng;Hou, Shuisheng

作者机构：

关键词： birds; genetics; genomics; plumage colour

期刊名称：MOLECULAR ECOLOGY （ 影响因子：4.9； 五年影响因子：5.6 ）

ISSN： 0962-1083

年卷期： 2023 年 32 卷 12 期

页码：

收录情况： SCI

摘要： Birds are among the most colourful terrestrial vertebrates, with various plumage colours and patterns. We conducted a genome-wide association study (GWAS) on an intercross F-2 population of Pekin ducks and mallards (n = 722) and identified a 1.57-Mb genetic region (Chr11: 20,176,480-21,750,101 bp) related to duck melanism. Fine mapping by linkage disequilibrium (LD) and F-ST analysis narrowed the final candidate region to a region of 22,500 bp (Chr11: 20,677,500-20,700,000 bp) including three coding genes, TCF25, MC1R and TUBB3. Combined with transcriptome and qRT-PCR analysis, MC1R was identified as the unique genetic locus responsible for black plumage in ducks, and it was significantly more highly expressed in the feather bulbs of black ducks. We also identified 52G > A (Chr11: 20,696,354G > A) and 376G > A (Chr11: 20,696,678G > A) mutations in the MC1R coding region that have been widely studied in ducks. In addition, structural variations (SVs) were screened by nanopore sequencing, and no significant SV was found to be associated with the duck black plumage trait. However, we identified four novel single nucleotide polymorphisms in the MC1R regulator region (Chr11: 20,678,412G > A, Chr11: 20,679,236G > A, Chr11: 20,692,496 A > G and Chr11: 20,692,791 A > G) that had a strong association with the black plumage phenotype of ducks and combined with potential changes in transcription binding affinities. The luciferase reporter gene assay demonstrated that Chr11: 20,678,412G > A and Chr11: 20,679,236G > A led to significant promoter activity changes. Our research emphasizes the importance of MC1R regulatory region mutation in determining the duck black plumage phenotype, and these results expand our understanding of the genetic mechanism underlying duck plumage colour.

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