Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
Poult Sci. 2024 Oct;103(10):104107. doi: 10.1016/j.psj.2024.104107. Epub 2024 Jul 17.
Plumage color is an intuitive external poultry characteristic with rich manifestations and complex genetic mechanisms. In our previous study, we observed that there were more dark variations in plumage color in the F population derived from the hybridization of 2 white duck varieties. Therefore, based on the statistics of plumage color of 308 F2 populations, we further used the resequencing data of these individuals to detect copy number variations (CNVs) in the whole genome and conducted genome-wide association studies (GWAS) to determine the genetic basis related to plumage color traits. The CNV detection revealed 9,337 CNVs, with an average length of 15,950 bp and a total length of 142.02 MB, accounting for approximately 12.91% of the reference genome. The CNV distribution on the chromosomes was relatively uniform, and the number of CNVs on each chromosome positively correlated with the length of the chromosome. In the pure black plumage group, 2,101 CNVs were only identified, and 1,714 were specifically identified in the pure white plumage group. Ten CNVs were randomly selected for validation using quantitative real-time PCR, and 9 CNVs had the same CNV types as predicted, with an accuracy of 90%. Based on GWAS, we identified 2 CNVs potentially associated with plumage color variations, with the associated CNV regions covering 9 genes. Enrichment analysis of these 9 candidate genes showed significant enrichment of 3 pathways (ribosome biogenesis in eukaryotes, RNA transport, and protein export) and 17 gene ontology terms. Among these, VWA5A can downregulate MITF by binding to the regulatory factors SOX10. The occurrence of CNV may indirectly contribute to duck plumage color variation by affecting the regulatory factors of the switch gene MITF in the melanogenesis pathway. These findings have improved the understanding of the genetic basis of duck plumage color variation and have been beneficial for developing and using plumage color traits in subsequent poultry breeding.
羽毛颜色是家禽直观的外在特征，表现丰富，遗传机制复杂。在我们之前的研究中，观察到由两个白色鸭品种杂交产生的 F 代群体中，羽毛颜色的深色变异较多。因此，基于 308 个 F2 群体的羽毛颜色统计数据，我们进一步利用这些个体的重测序数据，在全基因组范围内检测拷贝数变异（CNV），并进行全基因组关联研究（GWAS），以确定与羽毛颜色特征相关的遗传基础。CNV 检测发现了 9337 个 CNV，平均长度为 15950bp，总长度为 142.02MB，约占参考基因组的 12.91%。CNV 在染色体上的分布相对均匀，每条染色体上的 CNV 数量与染色体的长度呈正相关。在纯黑色羽毛群体中，仅鉴定到 2101 个 CNV，在纯白色羽毛群体中，特异性鉴定到 1714 个 CNV。随机选择 10 个 CNV 进行定量实时 PCR 验证，9 个 CNV 的 CNV 类型与预测结果相同，准确率为 90%。基于 GWAS，我们鉴定到 2 个与羽毛颜色变化相关的 CNV，相关的 CNV 区域覆盖 9 个基因。对这 9 个候选基因进行富集分析，显示出 3 个途径（真核生物核糖体生物发生、RNA 转运和蛋白质输出）和 17 个基因本体术语的显著富集。其中，VWA5A 通过与调控因子 SOX10 结合，下调 MITF 基因的表达。CNV 的发生可能通过影响黑素生成途径中转录因子 MITF 的调控因子，间接导致鸭羽毛颜色的变异。这些发现提高了对鸭羽毛颜色变异遗传基础的认识，有利于在后续家禽育种中开发和利用羽毛颜色性状。
