Transcriptional Profile And Small RNA Sequencing Analysis For Cotton Responses To Salt Stress And Drought Stress

As an important economic crop, cotton produces essential source fiber for textiles and seeds for oil. Due to dramatical effects on growth and yield, elucidation of possible mechanism response to water stress in cotton will be helpful for cotton breeding with strong resistance. In this study, transcriptome and small RNA analysises based on high-throughput techniques were used in upland cotton and Asian cotton, which could provide candidate genes for improving cotton resistance varieties.Upland cotton is one of the four cotton cultivars and is widely cultivated in the world. Here, the expression profilings that regulate salt stress in TM-1were monitored by GeneChip(?) Cotton Genome Array with samples taken from roots under100mM NaCl treatment. Microarray analysis showed that1503probe sets were up-regulated and1490probe sets were down-regulated when cotton seedling root exposed to100mM NaCl for3hours. Then, RT-PCR analysis validated42relevant/related genes. For studying related biological processes, GO enrichment analysis, MapMan analysis and comparative genomics analysis were used. According to enriched gene ontology terms, important processes such as the response to water stress, pathways of hormone metabolism and signal transduction pathways were induced by the NaCl treatment. Some key regulatory gene families such as WRKY, ERF, and JAZ were differentially expressed under abiotic and biotic stress. The transcriptome analysis might provide some useful insights into salt-mediated signal transduction pathways in cotton and offer a number of candidate genes as potential markers of tolerance to salt stress. A candidate JAZ gene from upland cotton was overexpressed in Arabidopsis and its function is studying.Gossypium arboreum (Asian cotton), a diploid cotton which shows characteristics in stress tolerance and good genetic stability, is a great breeding resource. MicroRNA is a regulatory element which is widely found in eukaryotic genomes, and can regulate gene expression at the transcriptional and post-transcriptional level. In this study, we sequenced and analyzed the small RNAs derived from leaf, stem, and root of Asian cotton seedling under salt stress and osmotic stress. We also compared the profilings of miRNA and their targets to find the potential regulatory mechanism. As a result,539miRNA were found response to water stress in three tissues. Among them394were differential expressed under PEG treatment while451under NaCl treatment. In addition, target genes were predicted for the539miRNA. Among the3419targets genes,3270genes were annotated by blast with NR database in NCBI. Many transcription factors were found regulated by miRNA, such as NAC, MYB,GRAS, bZIP and HD-ZIPⅢ. According to comparison profilings between miRNA and target gene, some of the target genes were negative regulated by miRNA. The most significant enrichment terms by GO analysis were "response to hormone" and "defense response". In addtion, we predicted618novel miRNA and their precusors’second structures using Mireap and RNAfold. Target genes were also predicted for those novel miRNAs. Many genes and miRNA playing key roles in water stress response were discovered using genechip and small RNA high-throughput sequencing. The result will enrich the knowleage of water stress response in coton and will be helpful for dissecting the mechanism under water stress.