A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks

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.