In silico approach to identification of a novel gene responsive to submergence stress in rice

Abstract

Submergence is one of the major constraints to rice production. Bioinformatics approach has been widely used to identify candidate genes on many biological aspects. In the present study, a novel gene involved in submergence stress in rice, Os07g47670 was identified by in silico approach. The amino acid sequence of Os07g47670 is highly homologous to hypoxia-responsive family proteins. No disordered regions are found in the Os07g47670 protein. In the Os07g47670 gene promoter, there are two ARE cis-regulatory elements, indicating that Os07g47670 is associated with submergence responsiveness. The Os07g47670 transcript levels are higher in roots of one or two-week old plants than in other tissues. Without the Sub1A gene, the expression level of Os07g47670 in M202 is low under submergence, ACC treatment, and normal condition. However, in the Sub1A genetic background, the Os07g47670 transcript level is strongly induced during submergence, and peaked at day 1 during submergence. The mRNA level of Os07g47670 in M202(Sub1A) was also significantly increased by ACC treatment. High expression level of Os07g47670 is correlated with the existence of the Sub1A gene. Os07g47670 shares similar expression patterns with Sub1A, ADH1, SLR1, and SLRL1 and are co-induced under submergence. Thus, we have documented Os07g47670 as a novel gene associated with submergence stress response. The identification of Os07g47670 will facilitate the understanding of the molecular mechanism of submergence tolerance in rice.

Key words: Rice (Oryza sativa L.), in silico approach, submergence, waterlogging.