Transcriptome and Metabolome Profiling Unveil Pigment Formation Variations in Brown Cotton Lines (Gossypium hirsutum L.)

Abstract

Naturally brown colored cotton (NBCC) is becoming increasingly popular due to its natural properties of coloration. However, poor fiber quality and color fading are key issues that are hindering the cultivation of naturally colored cotton. In this study, based on transcriptome and metabolome of 18 days post-anthesis (DPA), we compared the variations of pigment formation in two brown cotton fibers (DCF and LCF), with white cotton fiber (WCF) belonging to a near-isogenic line. A transcriptome study revealed a total of 15,785 differentially expressed genes significantly enriched in the flavonoid biosynthesis pathway. Furthermore, for flavonoid biosynthesis-related genes, such as flavonoid 3′5′-hydroxylase (F3′5′H), anthocyanidin synthase (ANS), anthocyanidin reductase (ANR), chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR), and chalcone isomerase (CHI), their expressions significantly increased in LCF compared with DCF and WCF. Moreover, transcription factors MYB and bHLH were significantly expressed in LCF and DCF. Most flavonoid-related metabolites (myricetin naringenin, catechin, epicatechin-epiafzelechin, and epigallocatechin) were found to be more highly up-regulated in LCF and DCF than WCF. These findings reveal the regulatory mechanism controlling different brown pigmentation in cotton fibers and elucidate the need for the proper selection of high-quality brown cotton fiber breeding lines for promising fiber quality and durable brown color pigmentation.

Integration of Metabolomic and Transcriptomic Analyses Reveals the Molecular Mechanisms of Flower Color Formation in Prunus mume

“…For instance, the identification of differential metabolites is employed to investigate the factors underlying the coloration of three distinct wheat grains, identifying cyanidin and peonidin as the principal anthocyanins responsible for color variation [ 16 ]. In the context of brown cotton fibers, most flavonoid-associated metabolites, such as myricetin, naringenin, catechins, epicatechin–epiafzelechin, and epigallocatechin, exhibit greater up-regulation than in white cotton fibers [ 17 ]. The composition and content of different flavonoid metabolites reveal the reasons for the flower color variation in Rhododendron pulchrum varieties [ 18 ].…”

Metabolome integrated with transcriptome reveals the mechanism of three different color formations in Taxus mairei arils

“…In our study, we observed a significant down-regulation of delphinidin-3-O-rutinoside in YTM compared with RTM, which may contribute to the diminished intensity of its red color. Epiafzelechin and lutein were also identified as the dominant factors in yellow pigments ( Lin et al., 2015 ; Lv et al., 2023 ). Similarly, our findings indicate a buildup of epiafzelechin and lutein in the YTM arils upon reaching maturity.…”