Wang Zhen, Guo Zhanbao, Liu Hongfei, Liu Tong, Liu Dapeng, Yu Simeng, Tang Hehe, Zhang He, Mou Qiming, Zhang Bo, Cao Junting, Schroyen Martine, Hou Shuisheng, Zhou Zhengkui
State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux 5030, Belgium.
Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giae114.
Plumage coloration is a distinctive trait in ducks, and the Liancheng duck, characterized by its white plumage and black beak and webbed feet, serves as an excellent subject for such studies. However, academic comprehension of the genetic mechanisms underlying duck plumage coloration remains limited. To this end, the Liancheng duck genome (GCA_039998735.1) was hereby de novo assembled using HiFi reads, and F2 segregating populations were generated from Liancheng and Pekin ducks. The aim was to identify the genetic mechanism of white plumage in Liancheng ducks.
In this study, 1.29 Gb Liancheng duck genome was de novo assembled, involving a contig N50 of 12.17 Mb and a scaffold N50 of 83.98 Mb. Beyond the epistatic effect of the MITF gene, genome-wide association study analysis pinpointed a 0.8-Mb genomic region encompassing the PMEL gene. This gene encoded a protein specific to pigment cells and was essential for the formation of fibrillar sheets within melanosomes, the organelles responsible for pigmentation. Additionally, linkage disequilibrium analysis revealed 2 candidate single-nucleotide polymorphisms (Chr33: 5,303,994A>G; 5,303,997A>G) that might alter PMEL transcription, potentially influencing plumage coloration in Liancheng ducks.
Our study has assembled a high-quality genome for the Liancheng duck and has presented compelling evidence that the white plumage characteristic of this breed is attributable to the PMEL gene. Overall, these findings offer significant insights and direction for future studies and breeding programs aimed at understanding and manipulating avian plumage coloration.
羽毛颜色是鸭子的一个显著特征，以白色羽毛、黑色喙和蹼足为特征的连城鸭是此类研究的理想对象。然而，对鸭子羽毛颜色遗传机制的学术理解仍然有限。为此，利用高保真 reads 对连城鸭基因组（GCA_039998735.1）进行了从头组装，并从连城鸭和北京鸭中产生了 F2 分离群体。目的是确定连城鸭白羽的遗传机制。
在本研究中，对 1.29 Gb 的连城鸭基因组进行了从头组装，contig N50 为 12.17 Mb，scaffold N50 为 83.98 Mb。除了 MITF 基因的上位效应外，全基因组关联研究分析确定了一个包含 PMEL 基因的 0.8 Mb 基因组区域。该基因编码一种色素细胞特异性蛋白，对黑素小体（负责色素沉着的细胞器）内纤维状片层的形成至关重要。此外，连锁不平衡分析揭示了 2 个可能改变 PMEL 转录的候选单核苷酸多态性（Chr33: 5,303,994A>G；5,303,997A>G），可能影响连城鸭的羽毛颜色。
我们的研究为连城鸭组装了高质量的基因组，并提供了令人信服的证据，证明该品种白羽特征归因于 PMEL 基因。总体而言，这些发现为未来旨在理解和操纵禽类羽毛颜色的研究和育种计划提供了重要的见解和方向。
