Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit.

Ali Moumeni,Ramiah Venuprasad,Arvind Kumar,Shoshi Kikuchi,Rachid Serraj,Kouji Satoh,Hei Leung

doi:10.1186/s12864-015-2335-1

Abstract

BackgroundDrought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different set of QTLs but contrasting drought tolerance levels in response to long-term drought-stress treatments. This work will help differentiate mechanisms of tolerance in contrasting NILs and accelerate molecular breeding programs to improve drought tolerance in this crop.ResultsThe two pairs of rice NILs, developed at the International Rice Research Institute, along with the drought-susceptible parent, IR64, showed distinct gene-expression profiles in leaves under different water-deficit (WD) treatments. Drought tolerance in the highly drought-tolerant NIL (DTN), IR77298-14-1-2-B-10, could be attributed to the up-regulation of genes with calcium ion binding, transferase, hydrolase and transcription factor activities, whereas in the moderate DTN, IR77298-5-6-B-18, genes with transporter, catalytic and structural molecule activities were up-regulated under WD. In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively. In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD.ConclusionsWe report here that the two pairs of NILs with different levels of drought tolerance may elucidate potential mechanisms and pathways through transcriptome data from leaf tissue. The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2335-1) contains supplementary material, which is available to authorized users.

Highlights

Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways
Water-deficit treatment and near-isogenic lines (NILs)’ physiological traits In the present study, we examined the effects of two WD treatments on the transcriptome changes and geneexpression profiles of the leaves of two pairs of NILs with contrasting drought tolerances at the reproductive stage
We observed from the reported results that among the two +QTLs NILs—including IR77298-14-1-2-B-10 and IR77298-5-6-B-18—that were tolerant to WD treatments, IR77298-14-1-2-B-10 showed a higher relative water content (RWC) [18] and a cooler canopy temperature [20]

Summary

Introduction

Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different set of QTLs but contrasting drought tolerance levels in response to long-term drought-stress treatments. Most of the high-yielding varieties grown in rainfed areas—IR36, IR64, MTU1010, Swarna, Samba Mahsuri, Sabitri, TDK 1—were bred for the irrigated ecosystem and never selected for drought tolerance. In drought years, these varieties have high yield losses, leading to a significant decline in rice production [6]. GO terms for molecular function binding, such as ‘coenzyme binding,’ ‘ATP binding’ and ‘transmembrane transporter activity,’ were significantly enriched in the up-regulated genes (Additional file 7). The expression pattern of the downregulated differentially expressed specific genes under moderate WD was similar to the expression pattern of those under severe WD, except that the genes involved in ‘heme binding’ were the most significantly enriched GO term

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