Abstract
Two indica inbred rice lines, IR64, a drought-sensitive, and Apo, a moderately drought-tolerant genotype, were exposed to non- (control or unstressed) and water-stress treatments. Leaf samples collected at an early flowering stage were sequenced by RNA-seq. Reads generated were analyzed for differential expression (DE) implementing various models in baySeq to capture differences in genome-wide transcriptional response under contrasting water regimes. IR64, the drought-sensitive variety consistently exhibited a broader transcriptional response while Apo showed relatively modest transcriptional changes under water-stress conditions across all models implemented. Gene ontology (GO) and KEGG pathway analyses of genes revealed that IR64 showed enhancement of functions associated with signal transduction, protein binding and receptor activity. Apo uniquely showed significant enrichment of genes associated with an oxygen binding function and peroxisome pathway. In general, IR64 exhibited more extensive molecular re-programming, presumably, a highly energy-demanding route to deal with the abiotic stress. Several of these differentially expressed genes (DEGs) were found to co-localize with QTL marker regions previously identified to be associated with drought-yield response, thus, are the most promising candidate genes for further studies.
Highlights
More than half of the world’s population depends on rice
Apo showed 0.95 between replicates under both non- and water-stress treatments. These results indicate a high level of reproducibility between replicates of the same genotype
Results using Shuhui and MSU v7 demonstrated that there were more IR64 genes responding to water stress including transcription factors (TFs) which were not found in Apo
Summary
More than half of the world’s population depends on rice. Most of these people live in Asia, where at least 90% of the world’s rice is produced and consumed [1]. While rice is generally adapted to a well-watered or irrigated ecosystem, there are genetic variations against drought that have been observed in traditional and modern varieties [4,5]. These phenotypic variations provide the platform for biological investigation to shed hints on the underlying genetic mechanisms of a drought response. DEbetween betweengenotypes genotypesusing usingaadifferent differentmodel modeltotocapture capture differences between two parental inbred lines across the environmental conditions Two parental inbred lines across the environmental conditions
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