In silico analysis and expression profiling for Resistance Gene Analogues (RGAs) and defence-related genes in early germinating conditions of rice against bakanae disease caused by Fusarium fujikuroi
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Date
2024-11
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CSIR-National Institute of Science Communication and Policy Research (NIScPR)
Abstract
Rice is a popular staple food in the world. Rice production is generally affected by many biotic and abiotic stresses. Among the biotic stresses affecting rice, bakanae has emerged as a serious challenge to Indian rice growers. Plant resistance gene analogues (RGAs) are genes with conserved domains and motifs that contribute to host resistance to disease. RGAs are frequently utilized in breeding programs and play a significant role in plant defence. The present study aimed to find out resistance gene analogues (RGAs) and other defence-related genes which might provide resistance to bakanae during the early germination stage of rice. A total of 32 gene IDs were selected from the previously reported transcriptome study of the bakanae-infected resistant and susceptible plants. The protein structures, active domains and biological functions were predicted via bioinformatical analysis. The predicted proteins were identified to possess one or more of the following features - hydrolase activity and carbohydrate metabolism, kinase activity, Rx_N domain, Rx_CC domain, NB-ARC domain, LRR domain, ADP/ATP binding site, and cytochrome site. Representatives of all the highlighted features were selected to prepare a set of 10 genes which were further evaluated for their expression in the inoculated seeds during germination via real-time PCR-based quantification. Four different rice genotypes viz, C101A51, Pusa 1342, PB1, and PB1121 with respective disease reaction types as highly resistant (HR), resistant (R), susceptible (S) and highly susceptible (HS) to bakanae were inoculated with two isolates of F. fujikuroi, F1121 and F1728. Based on the qPCR expression analysis of rice genotypes, RGA 2, RGA 5(b), and RGA 5(c) were found as potential candidate RGAs which might play role in providing resistance against bakanae in the early germination stage. Our study also identified one negative regulator i.e. GDSL esterase in the early stages of interaction due to its constant downregulation in different combinations of host-pathogen interactions. The outcome of this work will support the selection of essential RGAs and defence-related genes in resistance breeding programmes against bakanae disease.
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Keywords
Rice, Bakanae, Fusarium fujikuroi, Defence-related genes, RGAs, qPCR
Citation
Thakur Swagata, Syed Sharmeen Ekbal, Pandey Shashi, Sharma Sapna, S Gopala Krishnan, Saharan Mahendra Singh, Bashyal Bishnu Maya . In silico analysis and expression profiling for Resistance Gene Analogues (RGAs) and defence-related genes in early germinating conditions of rice against bakanae disease caused by Fusarium fujikuroi . Indian Journal of Biochemistry & Biophysics. 2024 Nov; 61(11): 714-730