Drought, which can induce osmotic stress, is the leading environmental constraint on crop productivity. Plants in both agricultural and natural settings have developed various mechanisms to cope with drought stress. The identification of genes associated with drought stress tolerance and understanding the underlying regulatory mechanisms are prerequisites for developing molecular manipulation strategies to address this issue. Here, we reported that the G-BOX FACTOR 14-3-3f (14-3-3 protein OsGF14f) positively modulates osmotic stress tolerance in rice (Oryza sativa). OsGF14f transgenic lines had no obvious change in crucial agronomic traits including yield and plant height. OsGF14f is transcriptionally induced by PEG treatment, and in rice, overexpression or knockout of this gene leads to enhanced or weakened osmotic stress tolerance, respectively. Furthermore, OsGF14f positively regulates abscisic acid (ABA) responses by interacting with the core ABA-responsive transcription factor BASIC LEUCINE ZIPPER 23 (OsbZIP23) to enhance its transcriptional regulation activity toward downstream target genes. Further genetic analysis showed that OsGF14f is required for the full function of OsbZIP23 in rice osmotic response, and OsGF14f-mediated osmotic stress tolerance partially depends on OsbZIP23. Interestingly, OsGF14f is a direct target gene of OsbZIP23. Taken together, our findings reveal a genetic and molecular framework by which the OsGF14f–OsbZIP23 complex modulates rice osmotic response, providing targets for developing drought-tolerant crops.

Although it is known that rice 14-3-3 family genes are involved in various defense responses, the functions of OsGF14f in response to diseases have not been reported. Here, we showed that the transcription of OsGF14f was significantly induced by leaf blast infection, and the overexpression of OsGF14f quantitatively enhanced resistance to leaf blast and bacterial blight in rice. Further analysis showed that the expression levels of salicylic acid (SA) pathway-associated genes (PAL1, NH1, PR1a and PR10) in the OsGF14f-overexpressing plants, were higher than those in wild-type plants after inoculation with the blast isolate (Magnaporthe oryzae Barr). In addition, the expression level of OsGF14f was significantly induced after SA treatment, and higher endogenous SA levels were observed in the OsGF14f-overexpressing plants compared with that in wild-type plants, especially after blast challenge. Taken together, these results suggest that OsGF14f positively regulates leaf blast and bacterial blight resistance in rice via the SA-dependent signaling pathway.

Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice.

Grain chalkiness is the main factor determining the market value of rice. Reducing chalkiness is an important breeding goal for genetic improvement of high quality rice. Identification of QTLs or genes controlling chalkiness is the prerequisite for molecular breeding in rice. Here, we conducted a genome-wide association study to identify QTLs associated with grain chalkiness including percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) in 450 rice accessions consisting of 300 indica and 150 japonica rice in two environments. A total of 34 QTLs were identified, including 14 QTLs for PGWC and 20 QTLs for DEC. Among them, seven QTLs were commonly identified in two environments, and eight QTLs were simultaneously related to two traits. Based on the haplotype analysis, LD decay analysis, RNA-sequencing, qRT-PCR confirmation and haplotype comparisons, four genes (LOC_Os10g36170, LOC_Os10g36260, LOC_Os10g36340 and LOC_Os10g36610) were considered as the candidate genes for qDEC-10c^1w,2wj, which could be identified in both environments and had the most significant p-value among the newly identified QTLs. These results provided new insight into the genetic basis of grain chalkiness and gene resources for improving quality by molecular breeding in rice.

Grain transparency (GT) is a key determinant of rice appearance quality and consumer preference, yet its genetic basis remains poorly understood. In this study, we evaluated GT in a panel of 450 rice accessions grown in two environments (Guangzhou and Yangjiang). Nineteen quantitative trait loci (QTL) for GT were identified by a genome-wide association study (GWAS), distributed across all rice chromosomes except chromosomes 2 and 12. Among these, four QTL (qGT-1b, qGT-3b, qGT-4b, and qGT-5b) were consistently detected in both environments. Notably, qGT-3b and qGT-5b co-localized with the grain shape genes GRAIN SIZE 3 (GS3) and GRAIN WIDTH 5 (GW5), respectively. For the novel and stable QTL qGT-4b, linkage disequilibrium decay analysis delimited an approximately 300 kb candidate region. Integrative transcriptomic and genomic analyses pointed to two candidate genes: LOC_Os04g40370 (OsFbx142), encoding an F-box domain protein, and LOC_Os04g40720 (OsSUBSrP1), encoding a subtilisin-like serine protease. Haplotype analysis further revealed that specific haplotypes of these genes were significantly associated with GT variation across environments. Our findings provide genetic insights into the regulation of rice grain transparency and offer candidate genes for further functional validation and potential application in improving rice appearance quality.

Seed vigor critically determines sowing performance, while grain quality fundamentally influences commercial value. Elucidating the genetic mechanisms governing these traits is critical for enhancing both seed vigor and grain quality in rice cultivation. Here, we demonstrate that the endosperm-specific gene OsEnS-42 is highly expressed in germinating seeds and developing seeds at the early filling stage. OsEnS-42 is localized in the nucleus and cytoplasm. The seed vigor of OsEnS-42 knockout plants decreased, manifested as decreases in germination rate, seedling length, and root length. In addition, OsEnS-42 knockout plants showed increased chalkiness and amylose content. The transcriptome and physiological indicators showed that OsEnS-42 regulates seed vigor through soluble sugars and redox metabolism, and regulates grain quality via soluble sugars and seed development-related enzymes. Haplotype analysis of OsEnS-42 across global rice germplasm revealed four distinct haplotypes (Hap 1–4) with subspecies-specific distributions. Crucially, accessions with Hap 4 exhibit a lower percentage of grain with chalkiness than accessions with Hap 1 (predominantly indica), enabling marker-assisted introgression to reduce chalkiness without subspecies barriers. Meanwhile, accessions with Hap 2 show lower amylose content, providing targets for specialty rice breeding. Our findings elucidate the pathways through which OsEnS-42 regulates seed vigor and grain quality, and provide new molecular breeding targets for improving seed vigor and grain quality in rice.