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

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 O-2-stressed roots of FR13A rice seedlings. The DSL was constructed from mRNAs isolated from the roots of low O-2-stressed FR13A rice seedlings from which pools of low-O-2-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.