Analysis Of Differentially Expressed Genes And Construction Of Gene Co-Expression Network In Rice Under Abiotic Stresses

Rice is one of the most important crops in the world as well as a monocotyledonous model plant and suffers various abiotic stresses during growth and development,which cause serious losses to the rice yield.Therefore,it is of great significance to cultivate stress-resistant rice varieties.Up to now,there is still a long way to go to have a comprehensive understanding of mechanism behind stress resistance in rice although many stress-related genes have been reported.To get a further understanding of mechanism behind stress resistance in rice,491 genechips related to various abiotic stresses have been collected from public databases and our laboratory.After obtaining differentially expressed genes(DEGs)under various abiotic stresses,we performed GO enrichment analysis and cis-element analysis of the promoters of these DEGs.Ultimately,we constructed gene co-expression networks under various abiotic stresses.The main results of the study are as follows:1.We have obtained DEGs under various abiotic stresses.There are 2506 DEGs under drought stress,2936 DEGs under cold stress,2259 DEGs under heat stress,2463 DEGs under salt stress and 174 DEGs are shared among four abiotic stresses.2.1.5kb sequences located in upstream of the transcriptional start site of the differentially expressed genes under various abiotic stresses were extracted as promoters and used for cis-element analysis.We have identified 26 cis-elements under drought stress,20 of which were highly similar with known motifs in the database and 6 of which had unknown functions.We have identified 16 cis-elements under cold stress,12 of which were highly similar with known motifs in the database and 4 of which had unknown functions.We have identified 17 cis-elements under drought stress,13 of which were highly similar with known motifs in the database and 4 of which had unknown functions.We have identified 24 cis-elements under drought stress,18 of which were highly similar with known motifs in the database and 6 of which had unknown functions.3.After calculating the gene expressions,we constructed gene co-expression networks under various abiotic stresses and identified the gene modules.We obtained candidate genes associated with various abiotic stresses by means of gene significance and module membership.We identified 13 gene modules and 200 candidate genes under drought stress,17 gene modules and 441 candidate genes under cold stress,22 gene modules and 139 candidate genes under heat stress,11 gene modules and 57 candidate genes under salt stress.