Investigation Of Cotton Fiber Development: Transcriptome And Metabolome Analysis

Cotton fiber, a secpified epidermal cell on cotton seeds, is an important crop product and also a model to study cell elongation and cellulose biosynthesis. To reveal features of cotton fiber development, we compared transcriptomes and metabolite profiles during fiber development.Comparative analyses of transcriptomes by 5k cDNA array identified 633 genes that are differentially expressed during fiber development. Principal component analysis (PCA) using expressed genes as variables divided fiber samples into four groups, which are diagnostic of developmental stages. The auxin responsive, wall-loosening and lipid metabolism are highly active during fiber elongation, whereas the cellulose biosynthesis is predominant and many other metabolic pathways are down-regulated in the secondary cell wall synthesis stage. Transcript and metabolite profiles and enzyme activities are consistent in demonstrating a specialization process of cotton fiber development toward cellulose synthesis. The li1 mutant has defects in auxin transport and only produces short fiber. In li1 fibers, most of the elongation stage-high genes are down-regulated, and the secondary cell wall synthesis is brought forward. In vitro auxin induces expression of elongation-related genes and represses secondary cell wall -related genes.Serial analysis of gene expression (SAGE) is then applied for further and more comprehentive analysis of fiber and ovule transcriptomes. 190,516 tags were obtained from cotton fiber, ovule (fiber deprived) and the fuzz-less lint-less (fl) mutant ovule; among them, 52,025 unique tags were identified. According to the copy numbers, 1,021 statisticaly significant unique tags were clustered and different expression patterns were deduced. Of the 309 typical tags enriched in fibers, 126 have been sequenced and 44 of them were fiber-high genes, indicating that SAGE can provide a large amount (>85%) of information for fiber study. Longer sequences were obtained from tags to poly (A) tails for 78 unmatched tags, which were then used for gene identification. 136 out of the 157 sequences are novel, indicating that SAGE is an efficient approach for isolation of novel transcripts of cotton. From the SAGE results, two IAA responsive gene tags are found with a fiber-high pattern and three Aux/IAA gene tags are identified with a fiber-repressed pattern, providing a possible link between cotton fibers enhanced auxin signal and the repressed expression of Aux/IAA genes.