Transcriptome Analysis of Pigment Related Genes in Colored Cotton

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 brown green and white 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 brown green and white cotton. The transcript level of all structural genes was higher in brown cotton fiber as compared to green and white at both 10 DPA (days post anthesis) and 20 DPA. The decline in the transcript level of all structural genes except GhANS was observed at 20 DPA as compared to 10 DPA. The transcript accumulation of GhANS was negligible in green and white cotton fibre at both stages. Correlating these findings with the flavonoid biosynthetic pathway revealed that GhANR and its substrate GhANS are crucial for the synthesis of proanthocyanadines which is a brown pigment and transcripts of structural genes are directly proportional to the brown pigment. In conclusion GhANS gene is strongly associated to the brown color development and modulation in the transcript level of this gene could improve the pigmentation of brown cotton fibers.