Differences of flavonoid structural genes preferentially expressed in brown and green natural colored cotton

We compared the expression levels of some structural genes involved in the flavonoid pathway between two brown cotton lines (brown 16 and light brown 14) and two green cotton lines (greenish 12 and light green 5). Gene expression levels of six structural genes F3’h (flavonoid 3ˈ-hydroxylase), F3’5’h (flavonoid 3ˈ5ˈ-hydroxylase), Dfr (dihydroflavonol 4-reductase), Lar (leucoanthocyanidin reductase), Ans (anthocyanidin synthase), and Anr (anthocyanidin reductase) were all substantially highly expressed in both brown cotton lines than in green cotton lines. Our study also revealed differences in expression levels between the two brown cotton lines. F3’h and F3’5’h had higher expression in the brown than in the light brown fibers, suggesting that increasing expression of these genes resulted in more of the proanthocyanidin pigments that give color to the brown lines. None of the genes examined were differentially expressed in the two green lines, suggesting the color difference is not due to products of the flavonoid pathway. The results suggest that breeding efforts to introduce brown colors into white-fiber lines with high-quality fiber focus on introgressing F3’h and F3’5’h and that naturally occurring allelic variants affecting the expression levels of these genes could be used to control the intensity of brown pigmentation

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