Genome-Wide Identification of Genes Responsive to ABA and Cold/Salt Stresses in Gossypium hirsutum by Data-Mining and Expression Pattern Analysis

For making better use of nucleic acid resources of Gossypium hirsutum, a data-mining method was used to identify putative genes responsive to various abiotic stresses in G. hirsutum. Based on the compiled database including genes involved in abiotic stress response in Arabidopsis thaliana and the comprehensive analysis tool of GENEVESTIGATOR v3, 826 genes up-regulated or down-regulated significantly in roots or leaves during salt or cold treatment in Arabidopsis were identified. As compared to these 826 Arabidopsis genes annotated, 38 homologous expressed sequence tags (ESTs) from G. hirsutum were selected randomly and their expression patterns were studied using a quantitative real-time reverse transcription-polymerase chain reaction method. Among these 38 ESTs, about 55% of the genes (21 of 38) were different in response to ABA between cotton and Arabidopsis, whereas >70% of genes had similar responses to cold and salt treatments, and some of them which had not been characterized in Arabidopsis are now being investigated in gene function studies. According to these results, this approach of analyzing ESTs appears effective in large-scale identification of cotton genes involved in abiotic stress and might be adopted to determine gene functions in various biologic processes in cotton.