Abstract
Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most critical diseases in rice. In order to study rice responsive genes to bacterial stress, microarray data were retrieved from GEO dataset. To identify the responsive genes to biotic stress (bacteria) bioinformatic tools were employed and the data presented in the forms of heatmap, gene ontology, gene network, and cis-element prediction were used. Almost all responsive genes were down-regulated at around 3 h time point and up-regulated 24 h time point in response to bacterial stress in rice varieties (Oryza sativa subs. japonica ‘IR64’, ‘IRBB5’, ‘IRBB7’ and ‘Y73’). Gene ontology showed that genes are involved in different biological processes including translation and cellular protein metabolic processes. Network analysis showed that genes expressed in response to pathogen infection (Xoo) included protein translation, eukaryotic initiation factors (eIFs), ribosomal proteins, protein ubiquitin, and MAPK genes. The genes expressed in response to bacterial stress can enable plant balance between synthesis and degradation of proteins which in turn allows plants for further growth and development. TATA-box and CAAT box had the highest number of cis elements involved in bacterial stress. These genes can provide novel insights into regulatory mechanisms in biotic stress responses in rice. Identification of bacterial stress response/tolerance genes of rice can assist the molecular breeding of new rice varieties tolerant to bacterial stress.
Highlights
Rice (Oryza sativa L.), the world’s most important staple crop, is the primary source of food for more than three billion people (Dawe, 2000)
Gene ontology analysis was carried out using the Singular Enrichment Analysis (SEA) tool offered by agriGO (Du et al, 2010)
We have suggested that RPL and RPS genes might be useful as candidate genes for manipulating stress tolerant rice varieties
Summary
Rice (Oryza sativa L.), the world’s most important staple crop, is the primary source of food for more than three billion people (Dawe, 2000). Rice production is affected by both biotic and abiotic stresses (Sharma et al, 2012). Rice has been used as a model crop in host-pathogen interactions, bacterial pathogenesis and defense responses in monocotyledonous plants (Li et al, 2006). High-throughput techniques have provided appropriate opportunities for detecting complex signaling pathways and genetic networks involved in response to biotic and abiotic stresses (Meena et al, 2017). Genes induced and expressed in response to abiotic and biotic stresses include eukaryote initiation factors (eIF3), the DEAD-box (eIF4), ribosomal proteins (RPL and RPS), MAPK kinases, peptidases, and ubiquitin genes. RPs have essential roles in stabilizing the ribosomal complex and mediating polypeptide synthesis in addition to extra-ribosomal functions such as their involvement in response to the environmental stresses (Sormani et al, 2011). Plants can balance between protein synthesis and degradation which in turn will allow them to grow further and develop
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