High yield and quality are two major goals in rice breeding programs. The key challenges facing breeding and functional genomics research in rice are the compatible improvement of both grain yield and quality. This work provides a comprehensive review of the advances in molecular genetic research on the co-regulation of grain yield and starch quality in rice. We summarize the genetic regulation of starch synthesis, scrutinize the molecular mechanisms of grain yield, examine the molecular mechanisms of co-regulation, and investigate the cloning and functional analysis of genes related to grain yield and quality. New approaches are proposed to address the trade-off between grain yield and quality, based on the discussion of previous research. The information will be valuable in overcoming the challenges related to grain yield and quality in rice using molecular breeding technology and will greatly facilitate the development of super rice varieties with high yield and good quality.

Bacterial blight (caused by Xanthomonas oryzae pv. oryzae) poses a serious threat to global rice production. In recent years, the prevalence of bacterial blight has been increasing in the South China rice-growing region, posing significant challenges to rice production safety. This study reviews the predominant pathotypes of bacterial blight isolates in the South China rice region, evaluates the bacterial blight resistance of commercially released rice varieties in this region, and summarizes the technologies and applications for improving broad-spectrum resistance to this disease. By systematically analyzing the pathogenic variation across subregions and the differences in variety resistance, this work aims to provide targeted breeding recommendations and practical references for enhancing resistance to bacterial blight. Finally, prospects for breeding bacterial blight-resistant rice varieties in South China are outlined.

RNA-binding proteins (RBPs) are key regulators of RNA metabolism and play crucial roles in various RNA processing events during cellular development in eukaryotes. They interact with RNA to form ribonucleoprotein complexes and can undergo phase separation, leading to the formation of dynamic, membrane-less condensates. This review begins by outlining the fundamental concepts of RBPs and phase separation. It then provides an in-depth analysis of the molecular mechanisms governing RBP-mediated phase separation in plant cells, highlighting its critical functions in plant growth, development, and responses to environmental stresses. Finally, the review discusses future challenges in researching RBP phase separation and its potential applications for crop improvement.

【Objective】This study aims to elucidate the function and mechanism of the ERF transcription factor OsERF93 in rice sheath blight resistance, providing genetic resources for disease-resistant breeding.【Method】The expression pattern, transcriptional regulatory function, and subcellular localization of OsERF93 were analyzed using RT-qPCR and transcriptional activation assays in rice protoplasts. Transgenic overexpression and knockout lines were constructed to investigate the role of OsERF93 in sheath blight resistance. Expression differences of salicylic acid (SA), jasmonic acid (JA), and ethylene (ET)-related signaling genes were compared before and after inoculation in transgenic lines. Additionally, agronomic traits of overexpression lines and controls were evaluated.【Result】OsERF93 was highly expressed in rice leaves and leaf sheaths and induced by sheath blight fungus infection. The encoded protein localized to the nucleus and cell membrane, exhibiting transcriptional activation activity. Overexpression of OsERF93 significantly enhanced sheath blight resistance, while knockout lines showed reduced resistance. JA biosynthesis gene OsAOS2 and certain PR genes were upregulated in overexpression lines and downregulated in knockout lines. Overexpression lines exhibited slightly reduced plant height and thousand-grain weight compared to wild-type controls but had significantly higher grain number per panicle. No significant differences were observed in tiller number, primary branch number, and panicle length between overexpression lines and controls.【Conclusion】The results indicate that OsERF93 positively regulates rice sheath blight resistance by activating the jasmonic acid signaling pathway, offering a novel genetic resource for rice disease-resistant breeding.

【Objective】The investigation of OsAlaAT4-mediated nitrogen utilization, contributes to an insight into the rice nitrogen regulatory network and supports the breeding of high nitrogen use efficiency rice varieties.【Method】Based on the amino acid sequence of OsAlaAT1, homologous genes were searched in the NCBI database. A knockout vector was constructed and transformed into Nipponbare (NIP) callus via Agrobacterium-mediated genetic transformation to obtain transgenic rice plants. Homozygous mutants were subsequently obtained. Wild-type Nipponbare (NIP) and mutant lines were grown in hydroponic systems at different nitrogen concentrations and in field trials to examine the relationship between OsAlaAT4 and nitrogen uptake and utilization.【Result】The homologous gene OsAlaAT4 was identified, and the knockout vector was successfully constructed and introduced into Nipponbare (NIP), resulting in two homozygous mutant lines. Hydroponic experiments at different nitrogen concentrations showed that the plant height, dry weight, and fresh weight of the mutant lines were lower than those of the wild-type under the same treatment, while the root length of mutant lines was higher. Under 1/2 standard nitrogen (N1/2), 4 times standard nitrogen (N4), and 8 times standard nitrogen (N8) treatments, the total nitrogen content of the mutant lines (alaat4-1 and alaat4-2) increased by 27.7%, 6.6%, 7.7% and 26.0%, 7.8%, 4.5%, respectively. The grain protein content of the mutant lines decreased by 3.0% and 3.3% under standard nitrogen conditions, respectively. Under low nitrogen field conditions, the plant height of the mutant lines was significantly lower than that of the wild-type. Compared to the wild-type, the nitrogen content in the leaves and stems of the two mutant lines increased by 12.1%, 13.5% and 14.4%, 6.9%, respectively, while the nitrogen content in the panicles decreased by 2.6% and 4.1%, and the yield decreased by 7.2% and 7.6%. Under high nitrogen field conditions, the number of tillers in the mutant lines was significantly higher than that of the wild-type. Compared to the wild-type, the nitrogen content in the leaves and stems of the mutant lines increased by 7.9%, 6.7% and 16.6%, 16.1%, respectively, while the nitrogen content in the panicles decreased by 4.9% and 4.5%, and the yield decreased by 6.5% and 5.4%. Under both low and high nitrogen conditions, the nitrogen use efficiency (NUE) of the mutant lines was lower than that of the wild-type.【Conclusion】Knockout of OsAlaAT4 resulted in increased nitrogen content in the leaves and stems of rice, but reduced nitrogen content in the panicles, protein content, and yield, resulting in reduced nitrogen use efficiency (NUE).

【Objective】Pre-harvest sprouting (PHS) severely compromises rice yield and grain quality, which is strongly influenced by seed dormancy genes. This study aims to elucidate the biological function of the seed dormancy gene Sdr4 and develop molecular markers for germplasm improvement, providing theoretical and practical insights for PHS-resistant rice breeding.【Method】A combination of bioinformatics analysis, molecular marker development, and marker-assisted selection was employed to systematically investigate Sdr4 functionality. Allelic variations between the strong-dormancy accession Kasalath and the weak-dormancy accession Nipponbare were analyzed to design genotype-specific markers.【Result】The Sdr4 promoter harbors core regulatory elements (e.g., TATA-box) and ABA-responsive cis-elements. The encoded protein is hydrophobic, exhibits low stability, and is extensively phosphorylated (25.93% within amino acids 101-150). Tertiary structure prediction indicated a composition of 15.50% α-helices, 15.50% β-sheets, and 66.37% random coils. Haplotype analysis of the 3K Rice Genome panel combined with AlphaFold modeling revealed that Sdr4 comprises six functional mutation-associated haplotypes. Furthermore, multiple amino acid sequence differences were identified in the Sdr4 protein between Kasalath and Nipponbare. Phylogenetic analysis demonstrated high conservation with Oryza glaberrima and Zizania palustris. Two functional markers (Sdr4-KF/KR and Sdr4-PF/PR) were developed to discriminate dormancy strength, and their efficacy was validated across 25 rice cultivars. Application of these markers in improving Zhongzhu 18 successfully generated novel lines with enhanced seed dormancy.【Conclusion】Sdr4 plays a critical role in regulating PHS resistance through the modulation of seed dormancy. Molecular screening confirmed weak dormancy phenotypes in 20 commercial varieties. The improved lines K17 and K88, developed via Sdr4-specific markers, exhibited significantly enhanced PHS resistance. This study establishes a framework for Sdr4 functional analysis and accelerates the molecular breeding of PHS-resistant rice germplasm.

【Objective】Rice blast is one of the most important diseases in rice production and poses a serious threat to global rice production. The large-scale and long-term planting of varieties with a single resistance gene often leads to the loss of resistance. Molecular marker-assisted selection is one of the most effective approaches for controlling rice blast..【Method】Using Taifeng B as the recipient, and Shuangkang 77009 carrying Pigm-1 and Digu B carrying Pid2 as donors, respectively. The genotypes of each generation were analyzed and identified by means of hybridization, backcrossing, backcrossing and recurred cross, aided by molecular marker-assisted breeding. Subsequently, the blast resistance of the developed sterile line Fumeng A and its hybrids was evaluated using 12 blast isolates from diverse sources under natural field conditions. Finally, through field trials, the fertility, main agronomic traits, combining ability, and heterosis of Fumeng A were systematically analyzed, and the photo-sensitive characteristics of its corresponding restorer line were also examined.【Result】A new three-line male sterile line, Fumeng A, carrying both Pigm-1 and Pid2, was developed. Inoculation tests both in the laboratory and field confirmed its blast resistance. Fertility identification showed that both the sterility rate and sterility degree of Fumeng A reached 100%, with a stigma exsertion rate of 57.39%. Genetic background and agronomic trait analysis indicated that Fumeng A inherited the main agronomic traits of the recurrent parent and exhibited improved yield potential. Heterosis analysis revealed that half of the hybrid combinations derived from Fumeng A yielded higher than the control variety Tianyouhuazhan, demonstrating good potential for production application.【Conclusion】Using molecular marker-assisted selection, a novel three-line male sterile line, Fumeng A (B), with high blast resistance, stable sterility, high stigma exsertion, and excellent agronomic and yield traits was developed. This work achieved targeted improvement of blast resistance in a sterile line and created a new parental material for three-line hybrid rice breeding.

【Objective】To study the molecular mechanisms of defense response and leaf premature senescence in rice,【Method】we screened a lesion mimic and early senescence mutant, designated lmes7 (lesion mimic and early senescence 7), from a mutant library of the japonica rice variety Wuyunjing 7. The main agronomic traits of the mutant and the photosynthetic pigment content in its leaves were measured. The target gene was identified through fine mapping and sequencing, and its encoded protein was analyzed and aligned.【Result】Physiological analysis showed that the photosynthetic pigment content in the mutant leaves was significantly lower than that of the WT, along with excessive accumulation of reactive oxygen species (ROS). In the lmes7 mutant, the effective tiller number, plant height, flag leaf length, flag leaf width, panicle length, grain number per panicle, seed setting rate, and grain yield per plant decreased significantly, while grain thickness increased significantly. Genetic analysis indicated that the mutant phenotype was controlled by a single recessive nuclear gene. Using map-based cloning, the target gene was fine-mapped to a 90-kb region between RM28486 and RM28489 on chromosome 12. PCR and sequencing revealed a 7-bp deletion in OsACL-A2, a gene encoding ATP-citrate lyase, in the lmes7 mutant, resulting in a frameshift mutation and premature termination of translation. Phylogenetic analysis and sequence alignment indicated that the mutation site of lmes7 lies within the succinyl-CoA synthetase domain, identifying lmes7 as a novel allelic variant of OsACL-A2.

【Objective】Seed storability is crucial for germplasm conservation, food security, and sustainable development. This study aims to identify QTLs associated with rice seed storability and explore the genetic basis of seed storability under different aging conditions.【Method】A set of 131 Oryza nivara introgression lines in the genetic background of the indica variety 93-11 was used. Seeds were subjected to natural aging and artificial aging treatments, and germination rates were measured for QTL mapping. RNA sequencing was performed to analyze genome-wide gene expression patterns in embryos from the storage-tolerant line Ra32 (carrying the O. nivara-derived allele of qASS1.1/qNSS1.1) and the storage-sensitive line Ra146 (without the allele). GO and KEGG enrichment analyses were conducted to explore enriched pathways and to identify genes related to seed storability.【Result】Six QTLs for seed storability were identified on chromosomes 1, 3, 6, 7, and 9, with individual QTLs explaining 3.3% to 21.0% of phenotypic variance. Among them, qASS1.1/qNSS1.1 was consistently detected under both natural and artificial aging treatments, and the O. nivara-derived allele at this QTL enhanced seed storability. Transcriptome analysis revealed 2077 differentially expressed genes (DEGs) under artificial aging and 1468 DEGs under natural aging, with 733 shared DEGs between the two treatments. GO and KEGG analyses showed that DEGs under artificial aging were enriched in 1428 GO terms and 97 metabolic pathways, while DEGs under natural aging were enriched in 1199 GO terms and 85 pathways. Two biological processes (circadian regulation of translation and hydrogen peroxide catabolic process) and 12 metabolic pathways (including MAPK signaling pathway, zeatin biosynthesis, histidine metabolism, and ascorbate and aldarate metabolism) were commonly enriched in both treatments, suggesting that seed storability may be regulated by antioxidant systems, energy metabolism, and accumulation of seed storage substances. Based on functional annotation of DEGs near the qASS1.1/qNSS1.1 locus, five candidate genes for qASS1.1/qNSS1.1 were further identified.【Conclusion】This study identified QTLs related to seed storability and screened multiple candidate genes, revealing that rice seeds enhance storability under different aging treatments mainly by regulating antioxidant defense, maintaining cellular stability, and modulating metabolic processes. These findings provide new genetic resources for improving seed storability in rice.

【Objective】Diurnal flowering time (FT) of rice is an important trait that affects the outcrossing rate and seed production yield of japonica rice sterile lines. This study aims to locate QTLs related to diurnal-floret-opening-time (DFOT) in japonica rice and analyze the pyramiding effects to clarify the main effect loci for DFOT traits.【Method】Recombinant inbred line populations consisting of 221 lines were constructed using japonica maintainer line J65B with early floret-opening-time and J139B with late floret-opening-time. The floret-opening-time was investigated in three years. QTL mapping analysis was conducted using genetic mapping and BSA-seq methods.【Result】A total of 30 DFOT QTLs were detected using complete interval mapping (ICIM) method on chromosomes 2−12. qFT5.2, qFT5.3, qFT5.5, qFT10.2, and qFT10.3 were major and stable QTLs which were detected simultaneously in more than eight environments, with an additive effect range of 13.04−50.93. Based on floret-opening time, extreme individuals were pooled for BSA-seq analysis. Association intervals related to floret-opening-time were detected in the regions of qFT5.3, qFT5.5, qFT6.2, and qFT10.2. According to the genotyping results, different progenies were divided into J139B type and J65B type in each QTL interval. QTL pyramiding effect analysis showed that QTLs derived from J65B would advance diurnal-floret-opening-time. The loci of qFT5.3 and qFT6.2 were essential for achieving early diurnal- floret-opening-time. The loci of qFT5.5 and qFT10.2 could further advance the diurnal-floret-opening-time.【Conclusion】Genetic mapping and BSA-seq analysis successfully identified four major stable QTLs related to rice diurnal-floret-opening-time. The localization of qFT5.3, qFT5.5, qFT6.2, and qFT10.2 establishes a foundation for further fine mapping and gene cloning and genetic improvement of diurnal-floret-opening-time in japonica rice.

【Objective】This study investigated the effects of different application time and rates of bud-promoting fertilizer on the quality of main crop rice and annual yield of ratoon rice to lay a basis for optimizing nitrogen management in ratoon rice cultivation for the coordination of high yield and high quality.【Method】A field experiment was performed using two rice varieties (Liangyou 6326 and Yongyou 4949), with two application time of bud-promoting fertilizer (early application at heading stage and normal application 15 days after heading) and two rates of fertilizer application (normal nitrogen rate of 75 kg/hm² and reduced nitrogen rate of 30 kg/hm²), to examine the growth of ratoon buds, dry matter accumulation, grain filling characteristics of the main crop, yield and rice quality.【Result】When applied at the normal time, the reduced rate led to a decrease in both ratoon and annual yields for both varieties, primarily due to reduced panicle number per unit area in the ratoon crop. Under early application with reduced rate, the effective panicle number and both ratoon and annual yields showed no significant differences compared to the normal application practice of bud-promoting fertilizer. Compared to the normal application practice, early application with reduced application rate of bud-promoting fertilizer lowered the grain filling rate in the main crop of both varieties, extended the active grain filling period of superior spikelets, increased the head rice percentage, decreased the percentage of chalky grains and chalkiness, and improved the appearance and processing quality of main crop rice. However, early application with the normal (high) rate of bud-promoting fertilizer resulted in a decrease in amylose content in Liangyou 6326, an increase in grain protein content, and a decline in cooking quality.【Conclusion】Early application with reduced rate of bud-promoting fertilizer enhanced the main-crop rice quality and obtained a similar annual yield as that under the normal application of bud-promoting fertilizer in two varieties. Therefore, optimizing application time and rate of bud-promoting fertilizer according to variety may synergistically improve main-crop rice quality and achieve high annual yield in ratoon rice production.

【Objective】In response to the problem that the existing integrated transplanting mechanism for picking and planting seedlings carries soil during operation, which affects subsequent seedling-picking and seedling-planting verticality, this study proposes a rice pot seedling transplanting method using dual mechanisms for seedling picking and planting.【Method】Firstly, based on the requirements for seedling picking, handover, and planting, several key pose points during the transplanting process were set as constraints for the picking and planting actions, and the motion trajectory was planned. Based on the principle of constant link length, a multi-position approximate motion synthesis model for a planar 2R mechanism was constructed. The particle swarm optimization (PSO) algorithm was used to solve for the optimal layout of the two rotating pairs of the mechanism, determine the rod length, and establish geometric constraints for the handover section. By combining the positions of the rotating pairs and the rod length parameters, the motion trajectory was reconstructed to solve the relative angular displacement between the two components and obtain the non-circular gear transmission ratio. To improve the concavity and convexity of the non-circular gear pitch curves, an objective function for the roundness coefficient of the pitch curves was established. The PSO algorithm was used to optimize the roundness of the non-circular gears, thus completing the design of the two-wheel mechanism for seedling picking and planting.【Result】Simulation analysis and bench tests of the mechanism showed that the maximum deviation between the actual motion trajectory and the theoretical trajectory is less than 1.8 mm, the error in the key pose clamping angle does not exceed 1.2°, and the transplanting success rate can reach 88.7%.【Conclusion】This study adopts a cooperative operation mode with separated picking and planting, which can effectively solve the problem of poor transplanting effect caused by soil carry-over in traditional mechanisms, and provides a new theoretical basis for the development of efficient rice pot seedling transplanting equipment.