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Drought is the major limiting factor for maize cultivation in India. Though many drought tolerant genotypes have been developed, there is very poor understanding of the tolerance mechanisms in these genotypes. Whole genome transcriptome analysis is an established high throughput genomic method employed for understanding complex traits like drought tolerance. We have employed RNA-seq analysis for understanding the drought tolerance of maize inbred line Z59 grown in kharif (wet season) and rabi (dry season). The physiological parameters recorded during the plant growth show difference in the values for relative water content and proline level but no significant changes were seen in root and shoot length. Leaf sample of irrigated and water stressed plants at reproductive stage were sequenced, transcripts were assembled, and the abundance were calculated. The results showed overall difference in expression level of genes in kharif (wet season) and rabi (dry season). The data was comparatively analyzed for genes differentially expressed between the irrigated and water stressed plants in both seasons. Taking p ≥ 0.001 and at least fourfold change in expression, a total of 453 and 774 genes were found to be differentially expressed amongst the irrigated and water stressed plants grown in kharif (wet season) and rabi (dry season)seasons respectively. Out of the 453 genes in kharif (wet season) grown plants, 227 genes were found to be up regulated and 226 genes were down regulated and in the 774 differentially expressed genes in rabi (dry season) grown plants, 460 genes were found to be up regulated and 314 genes were down regulated, in the water stressed sample when compared to irrigated. Functional annotation of these genes showed upregulation of MYB DNA binding protein and pathogenesis related protein in irrigated and early drought induced protein, late embryogenesis protein in water stressed kharif (wet season) crops. Metallothionein and aspargine synthetase are upregulated in irrigated and ubiquitin family protein, serine/threonine-protein kinase in water stressed rabi (dry season)crops. Gene ontology analysis co relates with the physiological parameters as most of the differentially expressed genes belong to the functioning of the plant when compared to the structural genes.
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