Analysis Of The Digital Gene Expression Profiling Of Cotton Fiber Development During Cell Elongation And Secondary Cell Wall Biogenesis

Cotton is the world's most important natural textile fiber and a significant protein and oilseed crop. Apart from their economic importance, cotton fibers provide an excellent single-celled model for studying plant cell elongation and cellulose biosynthesis. In recent years, many fiber-specific stage genes for fiber initiation and elongation have been isolated through both expressed sequence Tag (EST) analysis and microarray gene expression profiling. But little is known about the process of cotton fiber second cell wall (SWC) thickening.We adopted Tag-sequencing approach developed by Solexa to identify gene expression profiling during cell elongation and secondary cell wall biogenesis. Nine tag libraries (10DPA,15DPA,20DPA,23DPA,25DPA for line 69307 with high fiber strength and 10DPA,15DPA,20DPA,23DPA for line 69362 with low fiber strength), which came from two of the 196 recombinant inbred lines (sGK9708×0-153F6:8) with wide difference in fiber strength, were selected for sequencing. Each library was sequenced individually and generated more than 312 million Tags on average, which could be annotated for the genes through the comparison with the Unigene library for Upland cotton. Except for the gene number, the abundance of the gene was different. Each fiber development stage had its own distinctive features represented by regulatory genes. Some genes with evidently high expression level in fiber elongation stage were identified such as lipid transfer protein, metallothionein-like protein, aquaporin PIP1-2, and long chain fatty acid elongation enzyme. Some genes which play many major roles in cotton fiber SWC thickening were also isolated, including fasciclin-like arabinogalactan protein, cellulose synthase, Tubulin,1,4-beta-glucanase, fructose-bisphosphate aldolase, and so on. Quantitative real-time PCR were carried out to test and verify the genes differentially expressed between elongation and SCW thickening stage.Through analysis the tag sequences, the conclusions could be made as:(1) About 6% of Tag types account for nearly 70% of the total Tags, but 62% of Tags type was less than 8% of the total Tag number. This meant some specific genes play a significant role in the process of the fiber development. (2) Through the quantitiy RT-PCR for some genes, including beta-5 tubulin, beta-7 tubulin, sucrose synthase, metallotionein protein, cellulose synthase 1, cellulose synthase 2, aquaporin protein, Tag-sequencing could be considered to be accurate. (3) Through analysising the differential expressed genes in fiber elongation and SCW, there were significant differences in carbohydrate metabolism (including starch and sucrose metabolism, galactose metabolism, glycolysis/ gluconeogenesis and other glycan degradation), cytoskeleton regulation and Signal transduction. (4) Through analysing the differential expressed genes in SCW between the high fiber strength and the low fiber strength lines, it showed that the genes related to the phenylalanine metabolism, cytoskeleton regulation and sucrose synthase were immensely different, which indicated that they may play a crucial role in fiber SCW stage.