Isolation and transcription profiling of low-O₂ stress-associated cDNA clones from the flooding-stress-tolerant FR13A rice genotype

Abstract

Background and Aims: Flooding stress leads to a significant reduction in transcription and translation of genes involved in basal metabolism of plants. However, specific genes are noted to be up-regulated in this response. With the aim of isolating genes that might be specifically involved in flooding stress-tolerance mechanism(s), two subtractive cDNA libraries for the flooding-stress-tolerant rice genotype FR13A have been constructed, namely the single and double subtraction libraries (SSL and DSL, respectively). Methods: To construct the SSL, mRNAs present in the unstressed control FR13A roots were subtracted from the mRNA pool present in low O₂-stressed roots of FR13A rice seedlings. The DSL was constructed from mRNAs isolated from the roots of low O₂-stressed FR13A rice seedlings from which pools of low-O₂-stress up-regulated mRNAs from Pusa Basmati 1 and constitutively expressed mRNAs from FR13A roots were subtracted. Results: In all, 400 and 606 cDNA clones were obtained from the SSL and DSL, respectively. Global transcript profiling by reverse northern analysis revealed that a large number of clones from these libraries were up-regulated by anaerobic stress. Importantly, selective up-regulated clones showed characteristic cultivar- and tissue-specific expression profiles. Sequencing and annotation of the up-regulated clones revealed that specific signal proteins, hexose transporters, ion channel transporters, RNA-binding proteins and transcription factor proteins possibly play important roles in the response of rice to flooding stress. Also a significant number of novel cDNA clones was noted in these libraries. Conclusions: It appears that cellular functions such as signalling, sugar and ion transport and transcript stability play an important role in conferring higher flooding tolerance in the FR13A rice type.