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Genomic approaches to improve drought tolerance in rice: Strategies and perspectives

Arjula R. Reddy
Dept. of Plant Sciences, School of Life Sciences
University of Hyderabad, Hyderabad 500 046, A.P., India

Abstract

The complex traits such as drought tolerance are quantitative in nature and governed by a large number of genes dispersed across the genome. Owing to the multifactorial nature of the trait, the progress in discovery and elucidation of the role of each of those genes in the drought stress response processes has been rather slow. The completion of the whole genome sequence and the availability of high density molecular and genetic maps, well developed array procedures and simple transgenic protocols offer great opportunities for discovering candidate genes governing drought tolerance in rice. A combination of genetic, genomic and bioinformatic approaches can be effectively used to identify allelic variations and link them to the trait. We elaborate here such an integrated strategy and the progress of our work in three major areas of rice drought genomics and also project the way forward: 1) discovery of genes and identification of QTLs associated with drought stress response and gene expression profiling, 2) allelic variations at single nucleotide level in coding as well as regulatory regions of the target genes, and their association with the phenotype and 3) Functional validation through transgenics. In our gene discovery approach, we have generated a large collection of ESTs from the drought stressed seedling of a heat and drought tolerant rice genotype, Nagina22. In fact, more than half of the drought ESTs of rice (5815 out of 11,298) in public domain is represented from this library. The comparative analysis of our ESTs with the reported abiotic stress responsive gene orthologs enabled us to identify nearly 600 genes involved in drought stress response in rice. Further, this library served as a source for identification of EST-SSRs and SNP markers, and also for the construction of a cDNA chip with 15,552 features. Microarray expression profiling studies were carried at discrete stages of plant development at different levels of field drought stress. The data revealed at least 300 genes showing a change in expression levels ranging from 2 to 2000 fold in stressed plants. This data formed the basis for allele mining at the candidate loci. We have isolated and sequenced a number of putative promoters of several candidate genes from a panel of genotypes that are widely used in breeding for drought tolerance in India. Dissection of these identified allelic variations and their comparison with the known promoter elements revealed ABRE, Myb, GT1 and other elements associated with abiotic stress responses. Interestingly, a common haplotype pattern is observed in a group of genotypes that are phenotypically well characterized as drought tolerant. Currently we are genotyping a mapping population of rice using these sequence characterized SNPs and validating a few candidate genes including transcription factors for their functional role in planta in drought stress response processes. We propose a consortium approach to understand the role of candidate genes using genomic tools and exploit them in improving drought tolerance. We propose to focus on  the development of high throughput SNP platforms as a global network activity  for allele discrimination and genotyping. Further, the consortium may initiate another potential area of genomics research to discover and elucidate the role of microRNAs and epigenetic factors in regulation of drought stress responsive genes in rice.  (We acknowledge the support of Rockefeller Foundation and Dept of Biotechnology, Govt. of India).

 
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