Background: Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new varieties of glyphosate-tolerant crops is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire other glyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice. Results: Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg·ml^− 1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L + 1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L + 1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1). Conclusion: Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate in rice by regulating transcription and metal ions binding. These findings provide a theoretical basis for breeding glyphosate-tolerant rice varieties and for further research on the biogenesis of glyphosate- tolerance in rice.

Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of antioxidant systems, including glutaredoxin (GRX), that protect against various stressors. A total of 48 GRX gene loci have been identified on 11 of the 12 chromosomes of the rice genome; none were found on chromosome 9. GRX proteins were classified into four categories according to their active sites: CPYC, CGFS, CC, and GRL. In this paper, we summarized the recent research advances regarding the roles of GRX in rice development regulation and response to stresses, and discussed future research perspectives related to rice production. This review could provide information for rice researchers on the current status of the GRX and serve as guidance for breeding superior varieties.

Soil salinity is a key source of abiotic stress in the cultivation of rice. In this study, two currently cultivated japonica rice species—Zhegeng 78 (salt-tolerant) and Zhegeng 99 (salt-sensitive)—with similar backgrounds were identified and used to investigate their differential responses to salt stress at the post-germination and seedling stages. Quantitative RT-PCR analysis demonstrated that the expression of OsSOS1, OsHAK1, and OsHAK5 at the post-germination stage, and the expression of OsHKT1,1, OsHTK2,1, and OsHAK1 at the seedling stage, were significantly higher in the salt-tolerant Zhegeng 78 compared with those of the salt-sensitive Zhegeng 99 under salt stress. The significantly lower Na⁺ net uptake rate at the post-germination and higher K⁺ net uptake rates at the post-germination and seedling stages were observed in the salt-tolerant Zhegeng 78 compared with those of the salt-sensitive Zhegeng 99 under salt stress. Significantly higher activity of peroxidase (POD) and the lower hydrogen peroxide (H₂O₂) accumulation were observed in the salt-tolerant Zhegeng 78 compared with those of salt-sensitive Zhegeng 99 under salt stress at the seeding stage. The salt-tolerant Zhegeng 78 might be valuable in future cultivation in salinity soils.

Soil salinity is one of the major abiotic stresses limiting rice growth. Hybrids outperform their parents in salt tolerance in rice, while its mechanism is not completely understood. In this study, a higher seedling survival was observed after salt treatment in an inter-subspecific hybrid rice, Zhegengyou1578 (ZGY1578), compared with its maternal japonica Zhegeng7A (ZG7A) and paternal indica Zhehui1578 (ZH1578). A total of 2584 and 3061 differentially expressed genes (DEGs) with at least twofold changes were identified between ZGY1578 and ZG7A and between ZGY1578 and ZH1578, respectively, in roots under salt stress using the RNA sequencing (RNA-Seq) approach. The expressions of a larger number of DEGs in hybrid were lower or higher than those of both parents. The DEGs associated with transcription factors, hormones, and reactive oxygen species (ROS)–related genes might be involved in the heterosis of salt tolerance. The expressions of the majority of transcription factors and ethylene-, auxin-, and gibberellin-related genes, as well as peroxidase genes, were significantly higher in the hybrid ZGY1578 compared with those of both parents. The identified genes provide valuable clues to elucidate the heterosis of salt tolerance in inter-subspecific hybrid rice.

Egyptian rice landraces represent a unique genetic reservoir shaped by arid environments, yet their genomic and transcriptional response to salt stress remains largely unexplored. Here, we integrated genomic, transcriptomic, and population genetic analyses to systematically unravel the mechanisms of salt tolerance in this vital germplasm. Resequencing 56 Egyptian accessions uncovered a treasure trove of genetic variation, including 18,204 novel SNPs. An expanded GWAS on 258 accessions discovered 17 novel loci for salt tolerance. Parallel RNA-Seq analysis of a salt-tolerant-susceptible pair (Giza 176 vs. 9311) under stress delineated a defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype. The power of our integrated approach was exemplified by the convergent identification of ONAC063, where GWAS loci, transcriptional responsiveness, and haplotype-phenotype association collectively validated its role. Furthermore, selection sweep analysis highlighted 62 candidate genes under divergent selection. Our study not only positions Egyptian rice as a key resource for allele mining but also establishes a robust multi-omics pipeline for bridging genetic diversity with complex traits, accelerating the discovery of functional genes for breeding climate-resilient crops.

Pre-harvest sprouting (PHS) seriously compromises rice yield and quality, increase susceptibility to insect pest and reduce seed viability. Beside agronomic control measures, the genetic makeup of rice plants serves as a fundamental determinant in conferring resistance to PHS. Therefore, integrating multi-omics strategies to construct high-resolution genetic variation maps, screen extreme-phenotype germplasm, and identify causal genes are pivotal for generating PHS-resistant breeding material. In this study, we performed whole-genome re-sequencing of 165 highly diverse indica rice accessions to construct a high-density genetic variation map, obtaining a dataset comprising 1,584,905 high-quality SNPs for subsequent association analysis. Genome-wide association studies (GWAS) further uncovered 21 candidate loci and multiple candidate genes associated with PHS, from which key candidate genes were prioritized. In particular, previously cloned PHS-related genes— OsCDP3.10 , OsWRKY50 , UGT74J1 , OsJAZ6 , and IPA1 . Additionally, we investigated the transcriptional analyses in cultivars Z33 and Z216 under high-humidity conditions and identified 19,087 differentially expressed genes (DEGs). Notably, by integrating GWAS and transcriptomic analyses, we identified UGT74J1 as a promising candidate gene, and haplotype analysis further revealed UGT74J1 -Hap3 as a superior haplotype associated with PHS resistance. This multi-omics dataset and the candidate genes identified will provide valuable genetic resources for molecular breeding toward improved PHS resistance in rice.