Comprehensive Analysis of Glutamate Receptor-like Genes in Rice (Oryza sativa L.): Genome-Wide Identification, Characteristics, Evolution, Chromatin Accessibility, gcHap Diversity, Population Variation and Expression Analysis

Abstract

Glutamate receptors (GLR) are widely present in animals and plants, playing essential roles in regulating plant growth, development and stress response. At present, most studies of GLRs in plants are focused on Arabidopsis thaliana, while there have been few studies on rice. In this study, we identified 26 OsGLR genes in rice (Oryza sativa L.). Then, we analyzed the chromosomal location, physical and chemical properties, subcellular location, transmembrane (TM) helices, signal peptides, three-dimensional (3D) structure, cis-acting elements, evolution, chromatin accessibility, population variation, gene-coding sequence haplotype (gcHap) and gene expression under multiple abiotic stress and hormone treatments. The results showed that out of the 26 OsGLR genes, ten genes had the TM domain, signal peptides and similar 3D structures. Most OsGLRs exhibited high tissue specificity in expression under drought stress. In addition, several OsGLR genes were specifically responsive to certain hormones. The favorable gcHap of many OsGLR genes in modern varieties showed obvious differentiation between Xian/indica and Geng/japonica subspecies. This study, for the first time, comprehensively analyzes the OsGLR genes in rice, and provides an important reference for further research on their molecular function.

Functional characterization and allelic mining of OsGLR genes for potential uses in rice improvement

“…This is not unexpected as plants and animals represent distinct evolutionary lineages that diverged from a common ancestor more than a billion years ago. Consistent with our previous results ( Shi et al., 2022 ), the 26 GLR genes could be roughly classified into four groups ( Figure 1 ).…”

“…Sequences are available in the Supplementary Data 1 . Phylogenetic analysis of all plant GLRs and mammals iGluRs was conducted using the MEGA7.0 software ( Shi et al., 2022 ). Muscle sequence comparison, which is a logarithmic expected multi-sequence comparison method, was performed to compare the protein sequences of GLR proteins of the relevant species.…”

Why did glutamate, GABA, and melatonin become intercellular signalling molecules in plants?

“…A more recent analysis based on bioinformatic tools suggested the existence of 26 genes in rice that are related to the Arabidopsis GLRs. However, 3D and transmembrane domain predictions proposed that only 10–12 out of these actually show a GLR-like domain organisation ( Shi et al, 2022 ). Nevertheless, also in this case, the rice GLRs were divided into four subgroups.…”

Glutamate Receptor-like (GLR) Family in Brassica napus: Genome-Wide Identification and Functional Analysis in Resistance to Sclerotinia sclerotiorum

“…Glutamate receptor-like channels (GLRs), which are plant homologs of mammalian ionotropic glutamate receptors, are amino acid-sensing calcium channels [ 3 , 4 ]. The plant GLR gene family was first reported in A. thaliana , whose total 20 gene members were clustered into 3 major groups: AtGLR-I , AtGLR-II , and AtGLR-III [ 5 ]. Later, GLR gene families were identified in other plant species such as sugarcane [ 6 ], bean [ 7 ], rice [ 5 ], tomato [ 8 ], Rosaceae species [ 9 ], banana [ 10 ], cabbage [ 11 ], radish [ 12 ], soybean [ 13 ], and Brassica species [ 14 ].…”

“…The plant GLR gene family was first reported in A. thaliana , whose total 20 gene members were clustered into 3 major groups: AtGLR-I , AtGLR-II , and AtGLR-III [ 5 ]. Later, GLR gene families were identified in other plant species such as sugarcane [ 6 ], bean [ 7 ], rice [ 5 ], tomato [ 8 ], Rosaceae species [ 9 ], banana [ 10 ], cabbage [ 11 ], radish [ 12 ], soybean [ 13 ], and Brassica species [ 14 ]. Nevertheless, comprehensive characterization of motifs, PTM sites, and amino acid ligands and their binding pockets in GLR proteins has not yet been conducted.…”