Transcriptomics And Proteomics Studies On Cotton Fiber Initiation Induced With IAA And Ga₃in Vitro

Cotton is an important source of natural fibre used in the textile industry and plays a significant role in the global economy. Fiber development can be divided into four distinct and overlapping stages:initiation, elongation, secondary cell wall synthesis and maturation. Fibre initiation is a key period in determining cotton fiber initial number, and plant hormones play crucial roles in this process. Therefore, it is of high importance to investigate the effects of plant hormones on fibre initiation at both transcription level and protein level for revealing the molecular mechanisms underlying fibre initiation.Here we report the transcriptome profiling analysis of Xuzhou142-1DP A cultured in BT medium with0.5μM GA3、5μM IAA and0.5μM GA3+5μM IAA for1day and3days respectively by using Illumina sequencing in an attempt to gain insight into the molecular and cellular events associated with cotton fibre genes. Taking the ovules cultured in phytohormone-free media as control, RNA-seq analysis generated10,057significant differentially expressed genes (p<0.001,|log2Ratioj≥1). The results of Gene Ontology and pathway analysis show that a large number of genes related to DNA synthesis, sucrose metabolism, secondary metabolism, fat acid metabolism, tricarboxylic acid cycle, glycolysis, and carbon fixation were significantly different (p<0.05, q<0.05).2,330(23.2%out of all) differentially expressed genes participate in phytohormone synthesis and signaling transduction.1,670genes fall into67transcription factor families including103of bHLH,100of MADS,100of MYB-related,99of AP2-EREBP,85of FAR1,76of HB,73of C3H,73of MYB,70of WRKY,63of PHD,59of NAC,52of C2H2, and51of AUX/IAA transcript factors. Different transcription factors response differently to different hormone induction and cultutre period. By using Mapman analysis, we found a lot of genes encoding important enzymes involved in biosynthesis of Arabinogalactan, Pectic polysaccharide, Cellulose, hemicellulose in cell wall and genes in starch and sucrose metabolism including1sucrose phosphate synthase,2sucrose transporter,5UDP-glycosyl transferase,7Sucrose invertases neutral,3pfkB-type carbohydrate kinase family protein,1hexokinase,4glucose-1-phosphate adenylyl transferase,3starch synthase,2starch branching enzyme,2starch phosphorylase,4starch lyase, and one protein for starch transport.A total of1,299differentially expressed proteins (Ratio>1.3or<0.7, FDR<0.05) were identified through iTRAQ (isobaric tagging for multiplexed relative and absolute protein quantitation) analysis. The results of Gene Ontology and pathway analysis show that the differentially expressed proteins are mainly involved with a high degree of confidence (p<0.05, q<0.05) in ribosome assembly, oxidative phosphorylation, secondary metabolism, fat acid metabolism, tricarboxylic acid cycle, and carbon fixation. Network analysis using pathway studio5.0indicates that the direct interactions of the diffferentailly expressed proteins are focused on protein synthesis/folding/degradation, RNA processing, translation initiation/elongation, electron transfer, glycolysis, stress response, and transport. Through KEGG analysis, we Identified15cytoskeleton proteins including3Actins,4Actin-binding proteins,2Tubulins,2Tubulin-binding proteins,4annexins;5cytochrome P450proteins including2CYP73As,2CYP75Bs,1CYP98As; and13protein kinases including15’-AMP-activated protein kinase,2calcium-dependent protein kinases,1casein kinase1,6casein kinase Ⅱ subunit alpha,1extracellular signal-regulated kinase,1mitogen-activated protein kinase6,1TP53regulating kinase.