Transcriptomic analysis of root specific drought mediated response of G. arboreum and G. hirsutum

Gossypium hirsutum is a model species for domestication and genetic-engineering. Gossypium arboreum acts as a reference species for understanding G. hirsutum genome. Drought causes losses in crop productivity and requires its mitigation strategies. Microarray technology has been used in this study to identify the potential transcripts in G. hirsutum and G. arboreum under drought stress. G. arboreum and G. hirsutum plants were grown under drought stress and their drought specific genetic response was subsequently analyzed in the root samples. Customized 500 drought specific oligonucleotides were designed by cross species analysis of the Expression Sequence Tags (ESTs) of G. arboreum, G. hirsutum with Arabidopsis. An in-house microarray system was developed by printing the 500 drought specific oligonucleotides on glass substrate slides and probes were hybridized with the labeled cDNA of both the cotton species. In order to screen out drought responsive key elements, different bioinformatics tools analyzed and identified the upregulated and down regulated EST's in both the species. The functional characterization of EST's shows their association with different biological pathways involved for drought as well as other abiotic stresses. Real-Time PCR analyses showed the expression of the relevant transcripts responsible for different biological functions in root tissues under the drought stress condition. These results provide an insight to the root specific drought responsive differential expression of transcriptome between the two cotton species. Further characterization of upregulated transcripts will indicate the metabolism of these species to conserve energy during drought stress enabling them to survive longer during stress conditions.