Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Mol Ecol. 2023 Jun;32(12):3076-3088. doi: 10.1111/mec.16924. Epub 2023 Apr 16.
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 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 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.
鸟类是陆地脊椎动物中最具色彩的生物之一，具有各种羽毛颜色和图案。我们对北京鸭和绿头鸭的杂交 F1 群体进行了全基因组关联研究（GWAS）（n=722），并鉴定出一个与鸭黑化相关的 1.57-Mb 遗传区域（Chr11:20,176,480-21,750,101 bp）。通过连锁不平衡（LD）和 F 分析的精细作图，最终候选区域缩小到一个包含三个编码基因 TCF25、MC1R 和 TUBB3 的 22,500 bp 区域（Chr11:20,677,500-20,700,000 bp）。结合转录组和 qRT-PCR 分析，MC1R 被确定为导致鸭黑化的独特遗传基因座，其在黑羽鸭的羽芽中表达水平显著更高。我们还鉴定了 MC1R 编码区中的 52G> A（Chr11:20,696,354G> A）和 376G> A（Chr11:20,696,678G> A）突变，这些突变在鸭中已被广泛研究。此外，通过纳米孔测序筛选结构变异（SVs），但未发现与鸭黑化性状显著相关的 SV。然而，我们在 MC1R 调控区（Chr11:20,678,412G> A、Chr11:20,679,236G> A、Chr11:20,692,496 A> G 和 Chr11:20,692,791 A> G）中鉴定了四个新的单核苷酸多态性，它们与鸭黑化表型有很强的关联，并与转录结合亲和力的潜在变化相结合。荧光素酶报告基因检测表明，Chr11:20,678,412G> A 和 Chr11:20,679,236G> A 导致显著的启动子活性变化。我们的研究强调了 MC1R 调控区突变在决定鸭黑化表型中的重要性，这些结果扩展了我们对鸭羽色遗传机制的理解。
