| Cotton is an economically important crop for producing fiber essential for agriculture and textile industry. The high salinity is one of the major factors that limit photosynthesis and respiration, flowering, boll and fiber quality, and ion uptake in cotton, resulting in significant losses in yield. As a moderately salt-tolerant crop, upland cotton (Gossypium hirsutum L.) is recognized as a "pioneer crop" in saline soil and a suitable model plant to study mechanism of salt tolerance. There exist large differences of salt tolerance among cotton varieties. The response to salt stress is a complex biological process with multiple genes and factors involved. Currently, the possible regulatory pathways related to salt stress are not well understood in cotton. It is necessary to elucidate the possible molecular regulatory mechanism underlying the cotton response to high salinity, and further obtain some key genes from cotton genetic resources, which will be beneficial to improve salt tolerance of cotton.Affymetrix(?) Cotton Genome Array was used to compare the expression profiles of roots between salt tolerant variety "Zhong 07" and salt sensitive variety "Zhong G5" in response to salt stress for 3 h, 12 h and 48 h, with 36 chip data in total.2915 differentially expressed transcripts were identified by comparative analysis of 18 microarray data under the normal growth condition. Among them,1969 probe sets were up-regulated in roots of Zhong 07, with enriched GO terms related to amino acid metabolism and sugar metabolism. There were 961 up-regulated transcripts in the roots of Zhong G5, with the synthesis of sucrose enriched. We further performed comparative analysis between the two varieties under salt stress at different time points.1393 up-regulated and 1493 down-regulated probe sets were detected. The analysis results also showed that, in the salt tolerant variety "Zhong 07",395 probesets were up-regulated and 498 probesets were down-regulated under salt stress; in the salt sensitive variety "Zhong G5",513 probesets were up-regulated and 496 probesets were down-regulated under salt stress. Several probesets were selected for qRT-PCR validation and the results showed similar expression patterns. Further gene ontology (GO) enrichment analysis for those differentially expressed genes showed striking differences between the two varieties during 3,12, and 48 h salt stress. At the early stage after exposure to salt stress, Zhong G5 had a more rapid response to salt stress, with down-regulation of antioxidant-related transcripts, whereas the antioxidant-related probe sets showed no significant change in Zhong 07. With the extension of salt treatment time, the expression of antioxidant-related genes was induced in the Zhong 07 roots. After 48 h treatment with salt stress, the primary metabolic processes were repressed in Zhong G5, whereas secondary metabolic processes, in particular flavonoid and glucan metabolic processes, were down-regulated in Zhong 07. The above analysis results indicated that the dynamic expression profiles were significantly different in the roots of two varieties responded to salt stress. Their unique responses to salt stress might be related to their salt tolerant ability. The differential expression analysis also indicated that plant hormones and transcription factors might participate in response to salinity stress. Additionally, lipid metabolism, secondary metabolism, and various antioxidant enzyme genes might also play important roles in adaptation to salt stress.In the meanwhile, comparative analysis of salt and oxidative stress (Methyl Viologen, MV treatment) transcriptome was also conducted, and certain synergy between oxidative and NaCl stress was discovered. The differentially expressed transcripts were most involved in the synthesis of plant hormones, redox, transcriptional regulation, material transport and lipid metabolism processes, which regulating ion balance, osmotic balance and redox state.Additionally,315 public released and in-house microarray data were integrated together to build a co-expression gene network for 20480 probe sets. Network visualization was based on the Cytoscape (http://cytoscapeweb.cytoscape.org/). This network has been released through the GraP database. The co-expression network was applied to perform gene function prediction and annotation for the candidate genes related to salt tolerance in cotton. Considering the natural difference of the two cotton varieties and their transcriptional expression changes under salt stress, a number of candidate genes were selected for subsequent analysis and experimental verification.In summary, we conducted comparative transcriptome approach for studying the differential expression in the roots of two upland cotton varieties (Zhong G5 and Zhong 07) in response to salinity stress, and tried to elucidate the molecular regulatory mechanism underlying the cotton response to salt stress. We also found that there was a certain overlap in the response of cotton roots to salt stress and oxidative stress. Through combining our differential expression results together with co-expression network, a group of candidate genes with salt tolerance were identified and selected, which might provide gene resources and will be potentially beneficial for genetic improvement of cotton. This study might also provide an important reference for the study of salt tolerance mechanism in cotton root, and further promote the research of the mechanism in higher plants. |
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