RNA sequencing and genome-wide association analysis reveal key genes responsible for different feather colors in Youjiang goose.

Goose feathers have various colors, including black, white, brown, and gray, in addition to stripes and spots of different colors. The Youjiang goose is bred under specific ecological and climatic conditions in Jiangxi Province, China. Under natural circumstances, the Youjiang goose exhibits two colors of plumages, white and gray. This study employed RNA sequencing and Genome-wide association studies (GWAS) to analyze key genes of Youjiang goose feathers of white and gray colors to explore the underlying molecular mechanism of feather color synthesis. A total of 140 genes were differentially expressed in white and gray feathers. These genes were found to be associated with "Immunity, infection and inflammation" (DYNC1I1, HSPA8), "calcium ion binding" (EGFL6, PLA2G12B), "lipid and carbohydrate metabolism" (PAX3, COL3A1, COL6A1, TSHR, IGF1, NME3), and melanin metabolic process (TYRP1, EDNRB2, DCT, TYR, MLANA). The enriched gene ontology terms were "protein refolding", "extracellular region", and "signaling receptor binding". The top 3 enriched Kyoto Encyclopedia of Genes and Genomes pathways included the neuroactive ligand-receptor interaction (acyg04080), melanogenesis (acyg04916), and tyrosine metabolism (acyg00350). GWAS analysis revealed four single nucleotide polymorphisms (LOC125183578, VAMP7, LOC106047492, LOC106047519) on chromosome 13. These findings provide a basis for further investigation of goose feather color formation profiles.