Transcriptome And Proteome Analysis To Cotton Cultivars With Different Agronomic Characters During Fiber Initiation

Cotton fibers are single-celled trichomes that differentiate from the ovule epidermis. Cotton fiber development consists of four distinct but overlapping developmental stages: initiation, elongation, secondary wall deposition, and maturation. Cotton fiber yield and quality mainly depends on the first three processes, for example, fiber initiation determines the number of fibers in a single ovule; the elongation process largely determines the fiber length and relate to the quality formation in part. Cotton fiber cell development is a complex biological process that requires orchestrated changes in gene expression in developmental and physiological pathways. The results of EST sequencing and microarray analysis showed that up to several thousands genes are involved in fiber initiation and elongation. Although a number of genes mentioned above have been isolated and identified, the molecular mechanism of fiber development is far from being fully revealed, and gene function have not been directly linked to yield, fiber quality and other agronomic traits. Comparative gene expression (transcriptome) and protein expression (proteome) analyses in a certain stages of fiber development between upland cotton varieties (lines) with different genetic background and typical agronomic traits to identify differentially expressed genes and proteins, which can not only provide an opportunity to screen candidate genes that may be directly related to some agronomic traits and have potential value in use, but also provide candidate genes or proteins for expression QTL (eQTL) and protein QTL (pQTL) mapping in genetic genomics analyses to identify candidate key genetic loci controlling complex traits and construct the corresponding gene regulatory networks.In this paper, using five upland cotton varieties (lines) with obviously different agronomic characters of Xuzhou142, Suyan401,7235, CJ139and fuzzless-lintless mutant of Xuzhou142as research materials, we perform comparative RNA expression analyses and comparative protein expression analyses by gene chip technology and iTRAQ quantitative proteomics technology between four normal varieties (lines) during fiber initiation (0,1DPA) to screen differentially expressed genes that possibly be related to the formation of certain agronomic traits. Using the fuzzless-lintless mutant of Xuzhou142as the control, we identify the genes and proteins which consistently up-regulated or down-regulated in the normal wild types during fiber initiation by gene chip technology and iTRAQ quantitative proteomics technology as well, the major results are as follows:1. The Affymetrix Cotton GeneChip was used to compare the gene expression between four upland cotton varieties (lines) with typical agronomic traits in the fiber early development (0and1DPA). By screening criteria of q-value (%)≤5, Fold Change≥2or≤0.5, sample number≥3, a total of2331differentially expressed genes were identified. Among them,32genes are involved in cytoskeletal rearrangements,39genes are related to turgor maintenance,46genes link to hormone synthesis and signal transduction,84genes participate in glucose metabolism,22genes are responsible for intracellular reactive oxygen species homeostasis, and up to98genes care transcription factors.2. Using iTRAQ technology, we compared protein expression levels between three upland cotton varieties (lines) with typical agronomic traits of Suyan401,7235and CJ139during early fiber development (ODPA and1DPA), the fold changes of peptide mass peak area>1.2or<0.8are considered significant cutoff value,485and998proteins were identified by using PMF+MS/MS data to search against greenplant proteins in NCBInr protein database and cotton EST database respectively, the functions of the differentially expressed proteins arrange from binding activity, catalytic activity, molecular cell structure, translation regulation to cellular components of the assembly.3. In compasion of proteome and transcriptome data,240genes out of the2331differentially expressed genes are matched to270proteins. Only seven genes showed consistent changes in the transcriptome level and proteomics level, the correlation was very low. A possible explanation is that post-transcriptional modification, translation and post-translational modification mechanisms may play active roles in gene expression regulation during cotton fiber development.4. Taking Xuzhou142mutant as the control, we compared RNA and protein expression levels between normal wild types and the control. Using microarray, a total of293differentially expressed genes were identified, the functions of these genes enried in oxidoreductase activity, hydrolase activity, ion binding activity, nucleic acid binding activity and membrane transport activity. Using iTRAQ technology we identified406differentially expressed proteins, which involved in nucleic acid binding, protein binding, ion binding, oxidoreductase activity, hydrolase activity, transferase activity, cofactor binding and lipid binding activity.