Waxy rice is an important raw material in food processing, particularly for traditional Asian products such as rice balls. High-quality waxy rice powder, characterized by low levels of damaged starch and small particle size, is typically produced via wet grinding. However, this method generates substantial wastewater and consumes lots of energy, raising environmental concerns. In non-waxy rice, floury endosperm mutants have enabled high-quality rice powder through dry grinding, but this approach has not been extended to waxy rice. Here, a waxy rice mutant with floury-core endosperm was developed by an insertion mutation of the soluble starch synthase IIIa ( ssIIIa ) gene. Compared with the ssIIIa mutant of non-waxy rice, the waxy rice mutant exhibited distinct agronomic characteristics, including reduced yield-related traits. Nevertheless, the floury-core endosperm reduced starch damage and particle size in dry-ground flour, enhancing its suitability for waxy rice ball production. The mutant also contained more short chains and smaller molecules in amylopectin, associated with the upregulation of multiple ssIIIa -related genes. Those changes further resulted in decreased crystallinity and altered pasting and thermal properties. Waxy rice powder of the mutant was obtained via dry grinding and exhibited favorable processing and eating qualities. Dough was harder and easier to handle, while boiled balls were softer, less sticky, and easier to chew and swallow. Collectively, the floury-core endosperm modified agronomic traits, physicochemical properties, and gene expression in waxy rice, ultimately improving product quality. The dry grinding method using the mutant offers an environmentally friendly alternative to conventional wet grinding for high-quality waxy rice powder.

Boro II (BT), the first cytoplasmic male sterility (CMS) system in rice, is widely used in three-line japonica hybrid rice production. Accurate detection of maintainer-seed contamination in BT-type CMS seed lots is critical for ensuring genetic purity and hybrid seed quality. In this study, we developed a SYBR Green-based quantitative real-time PCR (qPCR) assay for the detection and quantification of maintainer-seed contamination in BT-type CMS seed lots. Maintainer-specific primers targeting a mitochondrial sequence unique to the maintainer line, together with an endogenous reference targeting a conserved mitochondrial sequence present in both maintainer and CMS lines, were validated for specificity. A standard curve was constructed using defined CMS-maintainer seed mixtures (0.1-5% contamination), and ΔCt values were converted to relative abundance (2-ΔCt). The assay exhibited high specificity, reproducibility, and sensitivity, with a strong linear relationship between 2-ΔCt values and actual contamination levels (R2 > 0.99). Performance testing using simulated contamination samples (0.2-3.13%) demonstrated accurate quantification with acceptable recovery rates. This method provides a rapid, robust, and reliable tool for routine genetic purity testing and quality control in BT-type CMS hybrid rice seed production.

Japonica soft rice varieties possess excellent eating quality, and their cultivation area has been steadily expanding in recent years. This study aimed to analyze japonica soft rice varieties cultivated in the Yangtze River Delta region of China at the genome level and to provide a theoretical basis for optimizing disease resistance and other important traits. Genotypic characterization and evaluation of ten major japonica soft rice varieties from the Yangtze River Delta region were conducted using a genome-wide single nucleotide polymorphism (SNP) chip. The experimental results indicated that the soft rice varieties in the Yangtze River Delta region had a relatively high japonica component and were all classified as typical japonica rice varieties. Specifically, the highest (95.6%) and lowest (91.5%) proportions of japonica genomic segments were detected in Tai’an 1 and Zhehexiang 2, respectively. Japonica soft rice varieties from Shanghai exhibited a closer genetic distance to those from Jiangsu Province than to those from Zhejiang Province. Genomic identity was highest between Tai’an 1 and Nanjing 46 (87.9%) and lowest between Tai’an 1 and Jia 67 (74.4%). Based on the results of the chip assay, a total of twenty-six functional genes controlling key traits, such as yield, quality, and resistance to biotic and abiotic stresses, were identified in the ten analyzed varieties. Among them, Zhehexiang 2 carried the broad-spectrum blast resistance genes Pi2 and Pita, which is useful for improving the blast resistance of japonica soft rice varieties. The findings of this study provide genetic resources and carrier materials for the efficient molecular improvement of japonica soft rice varieties.

Fusarium fujikuroi is the primary causal agent of rice bakanae disease, which can lead to substantial yield losses. Developing a rapid, highly specific, and accurate method for detecting F. fujikuroi is crucial for effective surveillance, prevention, and control of rice bakanae disease. In this study, a novel detection assay, RPA-Cas12a-F, was developed by integrating recombinase polymerase amplification (RPA) and Cas12a for the detection of F. fujikuroi. This assay demonstrated a limit of detection (LOD) of 1 copy/μL of reference plasmid or 0.1 fg/μL of F. fujikuroi genomic DNA (gDNA). Furthermore, to enable on-site detection, the RPA-Cas12a technique was combined with a lateral flow strip (LFS) for visual readout, thereby developing the RPA-Cas12a-LFS assay. The LOD of the RPA-Cas12a-LFS assay was 1000 copies/μL of plasmid or 10 fg/μL of F. fujikuroi gDNA. The RPA-Cas12a-based assays developed in this study enable rapid, highly accurate, sensitive, and specific detection of F. fujikuroi, making them a promising tool for on-site detection without the need for expensive equipment and time-consuming methodologies.

Plant height is a key agronomic trait influencing both seed production and yield in hybrid rice. In the elite japonica hybrid ‘Shenyou 26’, optimal plant height differences between the restorer line (‘Shenhui 26’) and the male sterile line (‘Shen 9A’) are critical for efficient pollination. In this study, we dissected the genetic basis of plant height variation using a doubled haploid (DH) population derived from ‘Shenyou 26’. Multi-environment phenotyping and QTL mapping identified seven QTLs associated with plant height, among which qPH1.1 and qPH9.1 were validated. qPH1.1 co-localized with the semi-dwarf gene SD1, and ‘Shen 9A’ carries a rare SD1-EQH allele that potentially confers reduced height relative to the SD1-EQ allele in ‘Shenhui 26’. qPH9.1 also contributed significantly to plant height variation, with the Shenhui26 allele increasing plant height in backcross validation. These findings indicate that plant height variation in ‘Shenyou 26’ is controlled by multiple loci, including SD1 allelic variants and other complementary QTLs, providing valuable resources for fine-tuning plant architecture in rice breeding.

The advancement of hybrid japonica rice is pivotal for securing japonica rice supplies and bolstering food security. To address prevalent issues such as inconsistent yields, subpar rice quality, and inadequate seed production in existing cultivars, Shenyou R3 was developed using advanced high-density rice gene chip technology, which is characterized by the expression of specific genes. This late-season, premium aromatic variety, characterized by a popcorn-like aroma, was bred by the Crop Breeding and Cultivation Research Institute of the Shanghai Academy of Agricultural Sciences. Shenyou R3 incorporates superior genes such as badh2-E7, Pi2, Xa21, Sdt97, and Hd17, among which, badh2-E7 and Hd17 are inherited from the maternal line, while Pi2, Xa21, and Sdt97 are inherited from both the maternal and paternal lines. Shenyou R3 offers high-quality rice that adheres to national premium grade 2 standards, with level 1 resistance to blast disease, and yields surpassing the control variety Huayou 14 by over 5% in 2022 Shanghai trials. The new hybrid japonica rice Shenyou R3 has high yield potential and nitrogen utilization efficiency. This paper elaborates on the molecular marker-assisted selection process, key traits, quality metrics, and yield performance of Shenyou R3, while also outlining essential cultivation practices.

Leaf morphology significantly impacts rice (Oryza sativa L.) plant architecture and yield. Here, we identified and characterized a novel narrow-leaf mutant, nal25, derived from indica rice cultivar ‘Huazhan’ using EMS mutagenesis. Phenotypic analyses revealed that nal25 exhibited significantly narrower leaves, reduced plant height, increased tiller number, and notably decreased grain size, seed setting rate, and thousand-grain weight compared to the wild type. Genetic analyses demonstrated that the narrow-leaf phenotype is controlled by a single recessive nuclear gene. Through precise localization analysis, the NAL25 gene was located within a region of approximately 103 kb on the long arm of rice chromosome 7. The sequencing results showed that the mutant nal25 had a T to C mutation at position 173 of the heat-shock protein gene LOC_Os07g09450 encoding the DnaJ domain in this interval, resulting in a change in amino acid 58 from leucine to proline. The qRT-PCR results showed that the expression level of NAL25 gene decreased in the mutant. The nal25 mutant obtained in this study exhibits stable mutant phenotypes, including dwarfism and excessive tillering, traits typically unfavorable for rice production. Nevertheless, it serves as valuable genetic material for forward genetics approaches to identify yield-related genes regulating leaf morphology and culm height. Thus, research on the nal25 mutant advances the development of rice varieties with ideal plant architecture, thereby stabilizing yield increases and safeguarding global food security.

The development of a new salt–alkaline-tolerant hybrid japonica rice is crucial for enhancing japonica rice supply and ensuring national food security. Utilizing molecular marker-assisted selection (MAS) technology combining Kompetitive Allele-Specific PCR (KASP) markers and a gene breeding chip, the salt-tolerant gene SKC1 was introgressed into a rice genotype Fan 14. This led to the development of Shenyanhui 1, a new high-quality, strongly heterotic, and salt-tolerant japonica restorer line. Subsequently, the high-quality, salt-tolerant japonica three-line hybrid rice variety Shenyanyou 1 was developed by crossing the BT-type japonica cytoplasmic male sterile (CMS) line Shen 21A with the restorer line Shenyanhui 1. Shenyanyou 1 carries the major salt tolerance gene SKC1, exhibiting excellent salt tolerance with seedling stage salt tolerance reaching level 5. Under precise salt tolerance evaluation throughout its growth cycle, Shenyanyou 1 achieved a yield of 3640.5 kg/hm2, representing an extremely significant increase of 20.7% over the control variety Yandao 21. Shenyanyou 1 exhibits superior grain quality, meeting the Grade 3 high-quality rice standards issued by the Ministry of Agriculture. Shenyanyou 1 has good comprehensive resistance, aggregating rice blast resistance genes such as Pi2, Pita, Pizt and LHCB5, bacterial blight resistance genes Xa26/Xa3, stripe blast resistance gene STV11, semi-dwarf gene Sdt97, nitrogen-efficient utilization gene NRT1.1B, the light repair activity enhancement gene qUVR-10, the cold resistance gene qLTG3-1, and the iron tolerance gene OsFRO1. It has good resistance to biotic and abiotic stresses. This paper details the breeding process, key agronomic traits, salt tolerance, yield performance, and grain quality characteristics of Shenyanyou 1.

Anther culture is a promising technique used in rice (Oryza sativa L.) breeding, although the genetic mechanisms associated with anther culturability remain elusive. In the process of in vitro anther culture, favorable alleles for anther culture are preferentially transmitted to doubled haploid (DH) populations, resulting in biased segregation of DH populations. Therefore, the segregation distortion (SD) method is an ideal approach for mapping the genetic loci controlling anther culturability. Performing a SD analysis using a genetic map consisting of 666 single nucleotide polymorphism markers, we identified five potential loci (logarithm of odds [LOD] > 3.5) that may be associated with anther culturability, including SDL2 and SDL3, which are overrepresented in japonica alleles, and SDL7, SDL9, and SDL11, which are overrepresented in indica alleles. In addition, nine pairs of epistatic interactions (EPIs) that contribute significantly (p < 0.05) to SD in the DH population were identified. Among them, the interaction between SDL2 and SDL3 is particularly noteworthy. These findings suggest that anther culturability in rice is governed by complex genetic mechanisms involving multiple nuclear genes and EPIs. This study provides insights into the genetic control underlying anther culturability in rice and lays the foundation for future research aimed at identifying causal genes associated with anther culturability.

Fragrant rice is favored deeply by consumers due to the strong fragrance. Fragrant rice is mainly caused by the loss-of-function mutation of the Betaine aldehyde dehydrogenase 2 ( Badh2 ) gene in rice. Badh2-E7 , with 8 bp deletion and 3 bp substitution in exon 7 of Badh2 , is the main mutation allele used in fragrant rice breeding. In this study, a genotyping method named RPA-badh2-E7 for Badh2-E7 allele was designed. This method has the characteristics of rapid (completed amplification in 5 min), sensitivity (100-fold than conventional PCR), no strict amplification conditions required (25 °C~45 °C), and independent of PCR amplifier (only one thermostatic incubator is enough for amplification). This method greatly improved the efficiency of molecular marker-assisted selection of rice fragrant genes and breeding of fragrant rice varieties.

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.

The development of Japonica hybrid rice is of great significance to ensure supply of good quality Japonica rice and food security in China. Aiming at the problems of late growth period, unstable yield, and the need to improve rice quality and seed production yield of Japonica hybrid rice, a new Japonica hybrid rice combination 'Shenyou28' with early maturity, good quality, blast resistance, stable and high yield and easy seed production was developed by using molecular breeding techniques including high-density rice gene chip. 'Shenyou28', bred by Shanghai Academy of Agricultural Sciences, is a three-line Japonica hybrid rice with 'Shen21A' as sterile line and 'Shenhui26-28' as restorer line. For two-year regional trials from 2018 to 2019, the average output were 10 588.5 kg/hm 2 , which was 11.6% higher than the control variety 'Huayou14'. For the one-year production trial, the output reached 10 473.0 kg/hm 2 , which was 4.8% higher than the control variety 'Huayou14'. 'Shenyou28' has good quality, reaching the second grade of national standard, and has fragrance because it carries fragrance gene badh2-p-5 ’ UTR . It also has good resistance to rice blast and bacterial blight because it aggregates the rice blast resistance genes Pi2 , Pita , Pib , Pi9 , Pi54 , Pikm , Pit , and bacterial blight resistance gene Xa21 . It was approved by the Crop Variety Certification Committee of Shanghai in 2020. The breeding process, variety characteristics and key points of high yield mechanized seed production technology of 'Shenyou28' are introduced in this study.

Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation distortion (SD) of chromosomal regions linked to these alleles in the doubled haploid (DH) population. Using the AC method, a DH population was generated from the japonica hybrid rice Shenyou 26. A genetic map consisting of 470 SNPs was constructed using this DH population, and SD analysis was performed at both the single- and two-locus levels to dissect the genetic basis underlying anther culturability. Five segregation distortion loci (SDLs) potentially linked to anther culturability were identified. Among these, SDL5 exhibited an overrepresentation of alleles from the female parent, while SDL1.1, SDL1.2, SDL2, and SDL7 displayed an overrepresentation of alleles from the male parent. Furthermore, six pairs of epistatic interactions (EPIs) that influenced two-locus SDs in the DH population were discovered. A cluster of genetic loci, associated with EPI-1, EPI-3, EPI-4, and EPI-5, overlapped with SDL1.1, indicating that the SDL1.1 locus may play a role in regulating anther culturability via both additive and epistatic mechanisms. These findings provide valuable insights into the genetic control of anther culturability in rice and lay the foundation for future research focused on identifying the causal genes associated with anther culturability.

稻谷的耐储性在种子生产保存和粮食储备中具有重要的意义.本研究以人工陈化的方法对15个三系杂交稻恢复系品种进行筛选,获得了繁11、繁12、繁31、繁32和繁38五个耐储性较好的品种.选择繁38与粳型恢复系繁26为亲本杂交获得F1代,构建了包含154个株系的双单倍体(double haploid,DH)群体.以2b-RAD简化基因组测序技术对亲本和群体中每个株系进行测序,并构建SNP标记遗传图谱.分析水稻在人工陈化10 d和15 d时与耐储藏相关的QTL.共检测到了6个与稻谷耐储性相关的QTL位点,分布于3号、5号、6号、11号和12号染色体上,LOD值介于3.4509～6.8036之间,可解释6.1575％～12.9979％的表型变异,加性效应在-6.7586％到6.1235％范围内.其中qSI-12位点在陈化10 d和陈化15 d两个条件下均能检测到.qSI-5a和qSI-6这2个位点只在陈化10 d时检测到,而qSI-3、qSI-5b和qSI-11这3个位点只在陈化15 d时检测到.此外,还检测到32对上位性互作位点.这些结果丰富了耐储性品种育种的遗传资源,为进一步精细定位耐储性相关的QTL奠定了基础.

Aphelenchoides besseyi (A. besseyi), a seed-borne parasitic nematode, is the causal agent of rice white tip disease (RWTD), which may result in a drastic loss of rice yield. Seed treatments are currently considered to be the most effective means of preventing the spread of RWTD. Therefore, the rapid, highly specific, and accurate detection of A. besseyi from rice seeds is crucial for the surveillance, prevention, and control of RWTD. Here, we describe a novel detection assay that combines recombinase polymerase amplification (RPA) and CRISPR/Cas12a to detect A. besseyi (termed RPA-Cas12a-Ab), with a low limit of detection (LOD) of 1 copy/μl of plasmid or 1:107 diluted DNA extracted from individual nematodes. To improve the user-friendliness, lateral flow strip assay (LFA) was adopted to visualize the detection result. The LOD of the RPA-Cas12a-Ab LFA assay was 1,000 copies/μl plasmid or 1:10 diluted DNA extracted from individual nematodes. The assay developed in this study was able to identify A. besseyi in 45 min with high accuracy and sensitivity without cross reaction with three closely related non-A. besseyi species. Thus, RPA-Cas12a-Ab is a rapid, sensitive, and specific detection system that requires no sophisticated equipment and shows promise for on-site surveillance of A. besseyi.

制种是杂交水稻推广过程中最为重要的环节之一,实现杂交粳稻全程高效机械化制种对保证杂交粳稻的持续、健康、快速发展具有重要意义.总结和归纳了杂交粳稻机械化制种的研究现状,分析了现阶段杂交粳稻机械化制种发展中存在的主要问题,对杂交粳稻全程机械化制种进行探索与实践,并介绍了上海杂交粳稻全程机械化制种的关键技术.

"紫祥优26"是由上海弘辉种业有限公司和上海市农业科学院联合选育的优质早熟晚粳稻新品种,于2018年通过上海市农作物品种审定.该品种熟期较早、熟相好,米质优、食味佳,植株矮、抗倒性强,分蘖能力强,丰产性好,适合在上海、苏南、浙北、皖南等地作单季晚稻或早茬口双季晚稻种植."紫祥优26"可直播栽培,也可育秧移栽,高产栽培中要注意适时早播、合理密植、科学用肥、加强病虫草害防治.

Marker-assisted selection or marker-aided selection（MAS） provides an effective complementary approach for conventional rice breeding with precise and speedy mobilization of target genes into elite genetic backgrounds. The targeted genes, however, may not be selected in the course of MAS due to the occasional recombination between the marker and the target gene/QTL during the many cycles of meiosis involved in breeding programs. This leads to failure in the selection of target traits（Gopalakrishnan et al, 2008）.

水稻是我国种植面积最大、总产量最多的粮食作物,发展杂交粳稻对于满足粳米供应,保障我国粮食安全具有重要意义.总结了我国杂交粳稻研究和发展历程,分析了制约杂交粳稻发展的主要技术瓶颈因素,概述了上海杂交粳稻研究的现状和特点,提出了上海杂交粳稻研究和产业发展的对策.

Clathrin-mediated vesicle trafficking (CMVT) is a fundamental process in all eukaryotic species, and indispensable to organism's growth and development. Recently, it has been suggested that CMVT also plays important roles in the regulation of plant immunity. However, the molecular link between CMVT and plant immunity is largely unknown. SCY1-LIKE2 (SCYL2) is evolutionally conserved among the eukaryote species. Loss-of-function of SCYL2 in Arabidopsis led to severe growth defects. Here, we show that mutation of OsSCYL2 in rice gave rise to a novel phenotype-hypersensitive response-like (HR) cell death in a light-dependent manner. Although mutants of OsSCYL2 showed additional defects in the photosynthetic system, they exhibited enhanced resistance to bacterial pathogens. Subcellular localisation showed that OsSCYL2 localized at Golgi, trans-Golgi network and prevacuolar compartment. OsSCYL2 interacted with OsSPL28, subunit of a clathrin-associated adaptor protein that is known to regulate HR-like cell death in rice. We further showed that OsSCYL2-OsSPL28 interaction is mediated by OsCHC1. Collectively, we characterized a novel component of the CMVT pathway in the regulation of plant immunity. Our work also revealed unidentified new functions of the very conserved SCYL2. It thus may provide new breeding targets to achieve both high yield and enhanced resistance in crops.