Comparative transcriptome analysis uncovers cell wall reorganization and repressed cell division during cotton fiber initiation.

BACKGROUND: Tetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand. RESULTS: Here, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutant Xu142fl during early lint fiber initiation period. Totally, 5516 DEGs including 1840 upregulated and 3676 downregulated were identified. GO enrichment analysis revealed that the downregulated DEGs were mainly associated with biological processes such as transcription related biosynthesis and metabolism, organic cyclic compound biosynthesis and metabolism, photosynthesis, and plant cell wall organization, with molecular functions involving transcription related binding, organic cyclic compound binding, and dioxygenase activity, while the upregulated DEGs were associated with DNA replication and phospholipid biosynthetic related processes. Among the 490 DEGs annotated as transcription factor genes, 86.5% were downregulated in the mutant including the Malvaceae-specific MMLs, expression patterns of which were confirmed during the central period of lint fiber initiation. Investigation of the 16 genes enriched in the cell wall organization revealed that 15 were EXPA coding genes. CONCLUSIONS: Overall, our data indicate that lint fiber initiation is a complicated process involving cooperation of multiple transcription factor families, which might ultimately lead to the reorganization of the cell wall and terminated cell division of the differentiating fiber initials.

Understanding the role of phytohormones in cotton fiber development through omic approaches; recent advances and future directions.

Cotton is among the most important fiber crops for the textile-based industry, thanks to its cellulose-rich mature fibers. The fiber initiation and elongation are one of the best models for deciphering mechanisms of single-cell differentiation and growth, that also target of fiber development programs. During the last couple of decades, high yielding omics approaches (genomics, transcriptomics, and proteomics), have helped in the identification of several genes and gene products involved in fiber development along with functional relationship to phytohormones. For example, MYB transcription factor family and Sus gene family have been evidenced by controlling cotton fiber initiation. Most importantly, the biosynthesis, responses, and transporting of phytohormones is documented to participate in the initiation of cotton fibers. Herein, in this review, the reliable genetic evidence by manipulating the above genes in cotton have been summarized to describe the relationships among key phytohormones, transcription factors, proteins, and downstream fiber growth-related genes such as Sus. The effect of other important factors such as ROS, fatty acid metabolism, and actin (globular multi-functional proteins) over fiber development has also been discussed. The challenges and deficiencies in the research of cotton fiber development have been mentioned along with a future perspective to discover new crucial genes using multiple omics analysis.