Transcriptomic and metabolomic profiling of flavonoid biosynthesis provide novel insights into petals coloration in Asian cotton (Gossypium arboreum L.)

Abstract Background Flower color affects insect pollination and the ornamental value of plants. Studying flower color improves the rate of plant hybridization and thus enriches the diversity of germplasm resources meanwhile, it also impacts the development of the horticultural industry. However, there is a clear lack of studies concerning intricate mechanism cotton flower-color differentiation. Hereby, we report an integrative approach utilizing transcriptome and metabolome concerning flower color variation in three Gossypium arboreum cultivars. Results A total of 215 differentially accumulated metabolites (DAMs) were identified, including 83 differentially accumulated flavonoid metabolites (DAFs). Colorless kaempferol was more abundant in white flowers, while gossypetin-fer showed specificity in white flowers. Quercetin and gossypetin were the main contributors to yellow petal formation. Pelargonidin 3-O-beta-D-glucoside and cyanidin-3-O-(6''-Malonylglucoside) showed high accumulation levels in purple petals. Quercetin and gossypetin pigments also promoted purple flower coloration. Moreover, 8178 differential expressed genes (DEGs) were identified by RNA sequencing. The correlation results between total anthocyanins and DEGs were explored and indicated that 10 key structural genes and 29 transcription factors promoted anthocyanin biosynthesis and could be candidates for anthocyanin accumulation. Finally, we constructed co-expression networks of key DAFs and DEGs, demonstrated the interactions between specific metabolites and transcripts in different color flowers. Conclusion This study provides new insights into elucidating the regulatory mechanisms of cotton flower color.