Drought is a major abiotic stress factors that reduces agricultural productivity. GRAS transcription factors are plant-specific proteins that play diverse roles in plant development. However, the functions of a number of GRAS genes identified in rice are unknown, especially the GRAS genes related to rice drought resistance have not been characterized. In this study, a novel GRAS transcription factor gene named OsGRAS23, which is located in a drought-resistant QTL interval on chromosome 4 of rice, was isolated. The expression of OsGRAS23 was induced by drought, NaCl, and jasmonic acid treatments. The OsGRAS23-GFP fused protein was localized in the nucleus of tobacco epidermal cells. A trans-activation assay in yeast cells demonstrated that the OsGRAS23 protein possessed a strong transcriptional activation activity. OsGRAS23-overexpressing rice plants showed improved drought resistance and oxidative stress tolerance as well as less H2O2 accumulation compared with the wild-type plants. Furthermore, microarray analysis showed that several anti-oxidation related genes were up-regulated in the OsGRAS23-overexpressing rice plants. The yeast one hybrid test indicated that OsGRAS23 could bind to the promoters of its potential target genes. Our results demonstrate that OsGRAS23 encodes a stress-responsive GRAS transcription factor and positively modulates rice drought tolerance via the induction of a number of stress-responsive genes.

Mechanized dry seeded rice can save both labour and water resources. Rice seedling establishment is sensitive to sowing depth while mesocotyl elongation facilitates the emergence of deeply sown seeds. A set of 270 rice accessions, including 170 from the mini-core collection of Chinese rice germplasm (C Collection) and 100 varieties used in a breeding program for drought resistance (D Collection), was screened for mesocotyl lengths of seedlings grown in water (MLw) in darkness and in 5 cm sand culture (MLs). Twenty six accessions (10.53 %) have MLw longer than 1.0 cm. Eleven accessions had the highest mesocotyl lengths, i.e. 1.4 – 5.05 cm of MLw and 3.0 – 6.4 cm in 10 cm sand culture, including 7 upland landraces or varieties. The genotypic data of 1,019,883 SNPs were developed by re-sequencing of those accessions. A whole-genome SNP array (Rice SNP50) was used to genotype 24 accessions as a validation panel, giving 98.41 % of consistent SNPs with the re-sequencing data in average. GWAS based on compressed mixed linear model was conducted using GAPIT. Based on a threshold of -log(P) ≥8.0, 13 loci were associated to MLw on rice chromosome 1, 3, 4, 5, 6 and 9, respectively. Three associated loci, on chromosome 3, 6, and 10, were detected for MLs. A set of 99 associated SNPs for MLw, based on a compromised threshold (−log(P) ≥7.0), located in intergenic regions or different positions of 36 annotated genes, including one cullin and one growth regulating factor gene. Higher proportion and extension of elongated mesocotyls were observed in the mini-core collection of rice germplasm and upland rice landraces or varieties, possibly causing the correlation between mesocotyl elongation and drought resistance. GWAS found 13 loci for mesocotyl length measured in dark germination that confirmed the previously reported co-location of two QTLs across populations and experiments. Associated SNPs hit 36 annotated genes including function-matching candidates like cullin and GRF. The germplasm with elongated mesocotyl, especially upland landraces or varieties, and the associated SNPs could be useful in further studies and breeding of mechanized dry seeded rice.

Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by −log₁₀(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.

Crop productivity is severely constrained by abiotic and biotic stresses, necessitating innovative strategies to enhance stress resilience. Glycerol-3-phosphate (G3P) is a central metabolite in carbohydrate and lipid metabolism, playing crucial roles in stress responses. In this study, we engineered a novel glycerol-3-phosphate dehydrogenase (GPDH) gene, designated OEGD, by fusing the N-terminal NAD-binding domain of rice OsGPDH1 with the feedback-resistant C-terminal catalytic domain of Escherichia coli gpsA. Overexpression of OEGD in rice enhanced tolerance to drought, phosphorus deficiency, high temperature, and cadmium (Cd²⁺) stresses, while also improving plant growth and yield under drought stress at the adult stage. Notably, the accumulation of glycerol-3-phosphate (G3P) and activities of antioxidant enzymes (SOD, POD, CAT) were significantly elevated in the transgenic plants following osmotic stimuli, and fatty acid profiles were altered, favoring stress adaptation. Transcriptomic analyses revealed that OEGD modulates cell wall biogenesis, reactive oxygen species (ROS) scavenging, and lipid metabolism pathways, with minimal disruption to core G3P metabolic genes. These findings highlight the potential of OEGD as a valuable genetic resource for improving stress resistance in rice.

Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs. In this study, a genome-wide association study (GWAS) for ETN was conducted on 270 rice accessions with 1,019,883 SNPs. Total of 214 SNPs were detected on eight rice chromosomes for ETN at a significance level of -log10(P) > 6.0. 12 QTLs associated with ETN were identified, including three known functional genes (e.g., D10, D27, Stvb-i) and one novel gene OsIAA3. Compared to wild-type plants, OsIAA3-overexpressing plants could significantly increase ETN in rice. In the natural population, haplotype analysis was conducted for D10, D27, Stvb-i, and OsIAA3, and their favorable alleles were identified. Molecular markers were also developed and validated within the natural population and bi-parent population, and the validation results demonstrated that the developed molecular markers can be utilized for marker-assisted selection breeding. This study not only enhances our understanding of the genetic regulatory basis of rice ETN but also provides excellent germplasm and favorable haplotypes that serve as valuable breeding resources and genetic material for improving ETN and yield in rice.