Whole genome resequencing uncovers candidate genes related to plumage color in Yuexi frizzled feather chicken.

Yuexi Frizzled Feather Chicken (YFC), an indigenous breed in China noted for its curly feathers, primarily comprises yellow, white, and black plumage color strains. However, the genetic mechanism underlying the regulation of plumage colors remains unknown. In this study, whole genome resequencing was employed to systematically analyze and evaluate the genetic diversity of these three distinctive plumage color strains, as well as to screen and identify crucial genes related to the plumage color. Population genetic structure analysis revealed that the YFC could be divided into 3 plumage color populations, with the yellow-feathered chickens showing the highest genetic diversity, whereas the black-feathered chickens exhibited the strongest signatures of artificial selection. Further, detection of selection signals through Fst, ROD, XPCLR indicated that 59 overlapping genes (including MC1R, CDH1, TCF25, and ZFHX3), 19 overlapping genes (including GRM5, TYR, CTSC, and RAB38), and 17 overlapping genes (including PTCH1, FBP1, and FBP2) were significantly associated with black, white, and yellow plumage color in YFC, respectively. GO annotation and KEGG pathway analysis indicated that the plumage color regulation primarily involved in cell adhesion and signal transduction, regulation and synthesis of melanin, and synthesis of biological molecules. Moreover, GWAS and Sanger sequencing revealed that the rs317806696 in the CDH1 gene was relevant to the black plumage color of YFC, while the rs317372610 and rs741501156 in the TYR gene was associated with the white plumage color. Hence, the objective of this study is to provide comprehensive genomic insights into the genetic diversity and plumage color regulation in YFC, which provide the foundation for protection of YFC genetic resources and selection of chicken breeding program for different plumage colors.