Drought responsive transcriptome profiling in roots of contrasting rice genotypes

Abstract

Drought avoidance is an important strategy exhibited by cereals for maintaining productivity under water deficit conditions. Most of the modern rice varieties stop their root growth during drought whereas few traditional cultivars have the ability to maintain root growth. An upland rice genotype Nootripathu was found to maintain its root growth under drought when compared to a shallow rooted IR20. Drought responsive transcriptome profiling of roots of IR20 and Nootripathu revealed that tolerant Nootripathu showed relatively more number of DEGs (4287) than susceptible IR20 (3081). Drought stress significantly affected expression of genes encoding cellulose synthases and expansins, two major gene families involved formation of cell walls in the shallow rooted drought susceptible genotype IR20. Genes involved in the biosynthesis of phytohormones namely ABA and Brassinosteroids were found to be significantly up-regulated in roots of Nootripathu during drought. Up-regulation of autophagy related genes involved in degradation of denatured/misfolded proteins in roots of IR20 indicates the severe progression of stress in IR20. Co-localization analysis of DEGs against QTL hotspots identified several putative candidate genes including a zinc finger domain containing protein, a bZIP transcription factor, a MYB factor and an OsMADS7 requiring further functional validation.