SNP discovery at candidate genes for drought responsiveness in rice


Characterization of single nucleotide polymorphisms (SNP) in candidate genes for drought tolerance is a promising approach for identifying alleles that are associated with drought phenotypes. For SNP discovery, we have used the technique of EcoTILLING contrasting diverse varieties to both japonica variety Nipponbare and indica variety IR64. Our germplasm panel of 1,536 Oryza sativa varieties covers the variety groups and eco-cultural types and includes parents of mapping populations used for drought QTL analyses.

A set of candidate genes for drought tolerance was identified through convergent evidence taking into account genome annotation, function, expression, and localization with a yield-component QTL under water stress. These genes include DREB2A, ERF3, trehalose-6-phosphate phosphatase, and actin depolymerizing factor among others.

EcoTILLING of a set of 900 of the Oryza sativa lines for 1,800 bp of coding and regulatory region of ERF3 identified a range of putative SNPs. Sequence confirmation from selected lines for each of the observed patterns identified 31 SNPs and short indels that grouped into nine haplotypes corresponding to variety types. Within-group association tests for drought-related traits were performed with one of the indica subgroups found to have a significant association with yield stability during water stress. Putative mismatches have been identified at 10 other candidate gene loci. Sequencing of these mismatches is under way to verify the SNP setting the stage for additional association tests of the SNPs with drought phenotypes.

In addition to SNP analysis of individual candidate genes, we will take a genome-wide approach to relate SNP haplotypic variation with expression polymorphism and phenotypes. Through a multiple-partner SNP discovery project, we expect to obtain genome-wide SNP haplotype data for 20 diverse rice genotypes, some of which are known to have contrasting phenotypic responses to drought stress. The combination of SNP and drought stress-transcriptome data may reveal causal relationships among SNP haplotypic blocks, expression polymorphisms, and adaptive responses to drought.


In: Drought frontiers in rice – Crop improvement for increased rainfed production (Serraj R, Bennett J and Hardy B, eds). World Scientific Publishing Co., Singapore, pp 311–324. ISBN: 978-981-4280-00-6 (DOI: 10.1142/9789814280013_0017).

SNP discovery at candidate genes for drought responsiveness in rice

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