Role of the type‐B authentic response regulator gene family in fragrant rice under alkaline salt stress

Abstract

Globally, rice is being consumed as a main staple food and faces different kinds of biotic and abiotic stresses such drought, salinity, and pest attacks. Through the cytokinin signaling, Type‐B authentic response regulators (ARR‐Bs) respond positively towards the environmental stimuli. ARR‐Bs are involved in abiotic stress tolerance and plant development but their molecular mechanisms in fragrant rice are still not fully explored. The current study showed the genome‐wide characterization of OsARR‐B genes under alkaline salt stress. Results showed that in total, 24 OsARR‐B genes were found and divided into four subgroups on the basis of a phylogenetic analysis. These genes were located on all rice chromosomes except 8 and 10. Analysis of gene duplications, gene structure, cis‐elements, protein–protein interactions, and miRNA were performed. Gene ontology analysis showed that OsARR‐B genes are involved in plant development through the regulation of molecular functions, biological processes, and cellular components. Furthermore, 117 and 192 RNA editing sites were detected in chloroplast and mitochondrial genes, respectively, encoding proteins of OsARR‐B. In chloroplast and mitochondrial genes, six and nine types of amino acid changes, respectively, were caused by RNA editing, showing that RNA editing has a role in the alkaline salt stress tolerance in fragrant rice. We also used a comparative transcriptome approach to study the gene expression changes in alkaline tolerant and susceptible genotypes. Under alkaline salt stress, OsARR‐B5, OsARR‐B7, OsARR‐B9, OsARR‐B10, OsARR‐B16, OsARR‐B22, and OsARR‐B23 showed higher transcript levels in alkaline salt tolerant genotypes as compared to susceptible ones. Quantitative RT‐PCR showed upregulation of gene expression in the alkaline tolerant genotypes under alkaline stress. Our study explored the gene expression profiling and RESs of two rice contrasting genotypes, which will help to understand the molecular mechanisms of alkaline salt tolerance in fragrant rice.

Genome-Wide Identification and Characterization of Receptor-Like Protein Kinase 1 (RPK1) Gene Family in Triticum aestivum Under Drought Stress

“…In silico prediction showed that TaRPK1 members were involved in several processes of development through regulation of molecular functions (MFs) and biological processes (BPs), and exhibited response to environmental stresses. Several prior studies also described that through monitoring expression of genes, microRNAs respond to stress stimuli ( Yan et al, 2019 ; Rasool et al, 2021 ; Rehman et al, 2022 ). The microRNAs are 21–24 nucleotides long endogenous non-coding RNAs that regulates development, growth, and adaptive response against abiotic stresses via monitoring target genes at posttranscriptional level or translation level of protein synthesis ( Bai et al, 2017 ).…”

Genome-Wide Analysis of the Type-B Authentic Response Regulator Gene Family in Brassica napus

“…Among the two main types of ARRs (A- and B-ARRs) involved in cytokinin signaling [ 37 ], type-B ARRs are transcription factors that can be activated by phosphorylation of the Asp residue in the receiver domain [ 1 ]. Hitherto, the B-ARRs have been studied in Arabidopsis , rice, tomato, tobacco, and peach, but not in oil crop B. napus [ 11 , 52 , 53 , 54 , 55 ]. In this study, 35 B-ARRs were identified in rapeseed based on the two conserved domains.…”

“…Recently, genome-wide identification, expressional analysis, and functional prediction of type B-ARRs in rice, tobacco, tomato, and peach have been reported [ 52 , 53 , 54 , 55 ]. However, the ARRs in Brassicas have not been studied.…”

Genome-wide and molecular characterization of the DNA replication helicase 2 (DNA2) gene family in rice under drought and salt stress

“…This identification was performed by using Gene Structure Display Server ( Guo et al, 2007 ). The analysis of conserved DNA2 motifs was performed by using MEME Suit (Multiple EM for Motif Elicitation) Version 4.12.0 ( http://meme-suite.org/tools/meme ) ( Rehman et al, 2022 ). Following parameters were used for this analysis: ten motifs to be found with motif width between 10 and 200; site distribution was one occurrence per sequence or set at zero (at most one occurrence for each motif was allowed for each sequence), whereas the maximum number of motifs was set to 10 ( Bailey et al, 2009 ).…”