Genomics of Naturally Colored Cotton: A Way Forward to Initiate Precision Breeding

Development of naturally colored cotton varieties has remained one of the major breeding objectives which will help in avoiding the use of dyes and chemicals for providing color to lint. In genetic stocks, only green- and brown-colored producing lint genotypes are available, thus restricting the development of naturally colored cotton related textile market. Further, little information about the inheritance and development of lint color formation as well as its association with fiber quality is the main obstacle in availability of elite naturally colored cotton germplasm. In this chapter, information regarding the inheritance of fiber color and its quality and the course of fiber color development are elaborated. In silico analyses have unraveled the structural difference, chromosomal location, and expression of genes related to flavonoid biosynthesis pathways in colored cotton. These genes are nonrandomly distributed in all chromosomes with a greater number of genes found in the At sub-genome. Gene structure revealed that closely related genes are similar in length and number of exon and intron, like all genes in PAL family having one intron. Expression analysis indicated that 24 genes are downregulated in both colored and white cotton fiber and generated separate group in heat map. In addition to this, it is concluded that the role of major flavonoid biosynthesis-related pathway genes GhC4H, GhCHS, GhCHI, GhF3H, GhDFR, and GhANR cannot be neglected to engineer different fiber colors. The generated information can be used to initiate precision breeding for introducing colored lint genes and/or inserting mutations in these genes using CRISPR-Cas in cultivated cotton species.