Expression Analysis of Fiber Pigmentation Genes in Cotton

Abstract The biochemical basis of pigmentation has been well studied in naturally colored cotton, but little is known about the molecular basis of color development in cotton fibers. The differences in pigmentation between white, khaki, shades of brown and shades of green cotton fiber can be mined by the molecular study of structural genes of flavonoid biosynthesis pathway. The transcriptome analysis of five flavonoid biosynthesis related structural genes, encoding chalcone isomerase (GhCHI), flavanone 3-hydroxylase (GhF3H), dihydroflavonol 4-reductase (GhDFR), anthocyanidin synthase (GhANS), and anthocyanidin reductase (GhANR) was performed at two fiber developmental stages i.e. 10 DPA and 20 DPA in white, khaki, dark brown, light brown, green, light green and dark green cotton. The transcript level of all structural genes was higher in brown cotton fiber as compared to green and white at all stages. The transcript accumulation of GhANS was negligible in green and white cotton fiber at both stages. Correlating these findings with the flavonoid biosynthetic pathway revealed that GhANR and its substrate GhANS are crucial for the synthesis of proanthocyanidins, which is a brown pigment and transcripts of structural genes are directly proportional to the brown pigment. Likewise, GhF3Hand GhDFR were found to be important for the creation of green color in cotton. In conclusion, GhANS is strongly associated with brown color development and GhF3H and GhDFR are associated with green color development. Modulation in the transcript level of these genes could improve the pigmentation of brown and green cotton fibers.