Analysis Of Expression Profiling And Transcriptome During Cotton Fiber Development

Gossypium hirsutum and Gossypium barbadense are the most commercially cultivated cotton in the world G. hirsutum occupies about90%of the cotton production in the world due to its high yield and strong adaptation to diverse environmental conditions. On the contrary, G. barbadense accounting for only5-8%of the production is much more expensive due to its unprecedented quality of the fiber length, fitness and strength. Gossypium hirsutum and Gossypium barbadense are allotetraploid cotton cultivars differing greatly in their fiber quality and developmental programs. Although a huge number of studies and approaches have been carried out to uncover the cotton fiber developmental mechanisms, it remains unclear how G. barbadense achieves its superior fiber characteristics. Because the transcriptome of the fertilized ovule at the day of anthesis reflects the cotton genome expression at the fiber initiation stage, we sequenced their ovule transcriptomes and analyed the fiber digital gene expression profiling of Gb21and Gh36from5DPA to25DPA (including5,10,15and25DPA). The results were as follows:1.Here we sequenced and analyzed their ovule transcriptomes, and obtained79,686ovule unigenes for G. hirsutum and67,450for G. barbadense.The confidence of these unigenes was confirmed by three independent analyses. First, comparison with the recently published diploid cotton reference genome showed that90.7%of diploid protein-coding genes are homologous to over three quarters of these ovule unigenes. Second, the ovule unigenes differentially assembled between the two cultivars were strongly enriched in post-embryonic development, consistent with their fiber developmental difference. The two transcriptomes each harbored over0.2million SNPs when mapped onto the diploid genome, consistent with the reported phylogenetic distance. SNPs between the two tetraploid cultivars were recovered to address their genetic difference. Strikingly, the unigenes with most nucleotide variation were those involved in post-embryonic development, and in fiber development including regulation of cell size and trichome differentiation. Therefore, this study provides a comprehensive list of unigenes for G. barbadense, and revealed hundreds of novel unigenes involving in the different fiber developmental mechanisms between the two cultivars.2.Based on the analysis of differential gene expression between different strains of cotton during the same period and the same period of two strains,the number of differentially expressed genes were similar in different periods of two cotton varieties. At5DPA and10DPA, the differentially expressed genes of Gossypium hirsutum and G. barbadense were1,924, of which1,419were up-regulated,505were down-regulated, During the period of10-15DPA, there were936differential expressed genes, only292up-regulated genes,644down-regulated genes. During the period of15-25DAP, there were2169differential expressed genes, only1,268up-regulated genes,901down-regulated genes.3. We performed the Gene Ontology (GO) analysis for the highly confidence differentially expressed genes between Gossypium hirsutum and Gossypium barbadense, discoved that the up-regulated hairy cell differentiation genes in the initial stage of ovule development and fiber elongation-related genes promote sea-island cotton fiber development. The fiber elongation stage of sea-island cotton was longer than the upland cotton also facilitates the sea-island cotton fiber development. According to the anlysis of similarities and differences of the sea island fiber related genes, found the genes and molecular mechanisms of sea-island cotton fiber quality superior to upland cotton.4. Furthermore,one MYB transcription factor GBMYB25and GbDET2were amplified from the sea-island cotton, and verified by sequencing, Blast alignment and homology analysis. By the analysis of real-time fluorescent quantitative PCR showed that the two genes GbMYB25and GbDET2were involved in regulating the fiber developmen.