Salt stress is one of the major constraints to rice cultivation worldwide. Thus, the development of salt-tolerant rice cultivars becomes a hotspot of current rice breeding. Achieving this goal depends in part on understanding how rice responds to salt stress and uncovering the molecular mechanism underlying this trait. Over the past decade, great efforts have been made to understand the mechanism of salt tolerance in rice through genomics, transcriptomics, proteomics, metabolomics, and epigenetics. However, there are few reviews on this aspect. Therefore, we review the research progress of omics related to salt tolerance in rice and discuss how these advances will promote the innovations of salt-tolerant rice breeding. In the future, we expect that the integration of multi-omics salt tolerance data can accelerate the solution of the response mechanism of rice to salt stress, and lay a molecular foundation for precise breeding of salt tolerance.

Background: CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice (Oryza sativa) remains limited. Methods: Using Arabidopsis CCCH proteins as references, we identified the CCCH gene family in rice and analyzed the physicochemical properties, subcellular localization, conserved structures, phylogeny, cis-regulatory elements, synteny analysis, spatiotemporal expression patterns, and expression patterns under drought, ABA, and MeJA treatments for the identified CCCH family members. Results: The results showed that the rice CCCH family comprises 73 members, which are unevenly distributed across the 12 chromosomes. Phylogenetic analysis classified them into 11 subfamilies. Subcellular localization indicated that most members are localized in the nucleus. The upstream regions of CCCH promoters contain a large number of cis-regulatory elements related to plant hormones and biotic stress responses. Most genes respond to drought, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. OsC3H36 was highly expressed under drought, ABA, and MeJA treatments. Haplotype analysis of this gene revealed two major allelic variants (H1 and H2), with H1 predominantly found in japonica rice and associated with increased grain width and 1000-grain weight. Functional validation using a chromosome segment substitution line (CSSL1) confirmed these findings. Conclusions: CCCH genes play important roles in rice growth, development, and stress responses. Additionally, we validated that OsC3H36 is associated with rice grain width and 1000-grain weight.

Soil salinization constitutes a major constraint on global agricultural production, with marked divergence in salt adaptation strategies between salt-tolerant barley (Hordeum vulgare) and salt-sensitive rice (Oryza sativa). This study systematically investigated the evolution and functional specialization of the C3HC4-type RING zinc finger gene family, known to mediate abiotic stress responses through E3 ubiquitin ligase activity, in these contrasting cereal species. Through comparative genomics, we identified 123 HvC3HC4 genes and 90 OsC3HC4 genes, phylogenetically classified into four conserved subgroups. Differences in C3HC4 genes in phylogenetic relationships, chromosomal distribution, gene structure, motif composition, gene duplication events, and cis-elements in the promoter region were observed between barley and rice. Moreover, HvC3HC4s in barley tissues preferentially adopted an energy-conserving strategy, which may be a key mechanism for barley’s higher salt tolerance. Additionally, we found that C3HC4 genes were evolutionarily conserved in salt-tolerant species. The current results reveal striking differences in salt tolerance between barley and rice mediated by the C3HC4 gene family and offer valuable insight for potential genetic engineering applications in improving crop resilience to salinity stress.

Grain number per panicle (GNPP), determined mainly by panicle branching, is vital for rice yield. The dissection of the genetic basis underlying GNPP could help to improve rice yield. However, genetic resources, including quantitative trait loci (QTL) or genes for breeders to enhance rice GNPP, are still limited. Here, we conducted the genome-wide association study (GWAS) on the GNPP, primary branch number (PBN), and secondary branch number (SBN) of 468 rice accessions. We detected a total of 18 QTLs, including six for GNPP, six for PBN, and six for SBN, in the whole panel and the indica and japonica subpanels of 468 accessions. More importantly, qPSG1 was a common QTL for GNPP, PBN, and SBN and was demonstrated by chromosome segment substitution lines (CSSLs). Considering gene annotation, expression, and haplotype analysis, seven novel and strong GNPP-related candidate genes were mined from qPSG1. Our results provide clues to elucidate the molecular regulatory network of GNPP. The identified QTLs and candidate genes will contribute to the improvement of GNPP and rice yield via molecular marker-assisted selection (MAS) breeding and genetic engineering techniques.

Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe–metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.

Drought is a major abiotic stress limiting rice production worldwide. GA2ox3, a GA 2-oxidase involved in gibberellin deactivation, has been previously linked to growth regulation. Here, we demonstrate that functional disruption of GA2ox3 enhances shoot growth but compromises drought tolerance in rice. CRISPR/Cas9 knockout lines (ga2ox3) showed increased plant height and reduced antioxidant capacity under 20%PEG-induced osmotic stress, evidenced by higher H₂O₂ and MDA accumulation and decreased POD activity. Moreover, expression analysis revealed that GA2ox3 may be associated with the GA signaling cascade involving OsSLR1, OsBURP3, and OsSUS1. Haplotype analysis based on 627 rice accessions identified two major alleles, Hap1 and Hap2, with Hap1 showing higher GA2ox3 expression and stronger drought resilience. These findings suggest that GA2ox3 positively regulates osmotic stress tolerance, and its natural variation represents promising genetic resources for improving drought adaptation in rice.