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Plant Prime Editing: A New Direction in Crop Breeding SONG Anqi, WU Songquan, MA Qiuyue, BAN Wanning, LIU Xiangguo, JIN Yongmei Chinese Journal OF Rice Science    2025, 39 (6): 711-730.   DOI: 10.16819/j.1001-7216.2025.241005 Abstract （808）   HTML （36）    PDF （2292KB）（677）       Knowledge map    Save Plant Prime Editing (PPE) provides a novel approach for precise genome modification in plants, overcoming the limitations of conventional gene editing methods that rely on double-strand breaks and exogenous donor DNA. It enables not only arbitrary base substitutions, but also precise insertions and deletions of small to large DNA fragments, with reduced off-target effects. This review systematically summarizes the latest research advances in PPE technology globally, including its development history and working mechanism, applications in crop breeding and trait improvement, and representative cases. It also discusses the expansion of prime editing into large-scale genome editing and multiplex gene editing. To address the bottlenecks faced by PPE systems in plant genetic transformation, several potential solutions are proposed. Finally, the broad application prospects of PPE technology in plant genetic improvement and its potential integration with artificial intelligence (AI) in future research are outlined. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Flowering Habits of Rice and Its Application in Breeding japonica Cytoplasmic Male Sterile Lines CHEN Ling, LIN Wenying, LIANG Limei, OUYANG Younan, YE Shenghai, JI Zhijuan Chinese Journal OF Rice Science    2025, 39 (6): 731-743.   DOI: 10.16819/j.1001-7216.2025.241120 Abstract （575）   HTML （27）    PDF （1296KB）（626）       Knowledge map    Save The utilization of heterosis has significantly increased the yield of rice. Hybridization between indica and japonica subspecies exhibits stronger heterosis due to their distant genetic relationships. Consequently, indica-japonica hybrid rice has greater yield potential. Inter-subspecies hybridization between indica and japonica is an important way to enhance rice yields. Currently, indica-japonica hybrid rice mainly refers to the combinations derived from crossing a japonica cytoplasmic male sterility (CMS) line with an indica restorer line. These combinations have received widespread attention in production because of their vigorous growth, ideal plant architecture, resistance to premature senescence, and super high yield advantages. However, the japonica CMS line is characterized by its flowering habits, such as low stigma exsertion rate and late flowering time. These habits lead to asynchronous flowering time between the indica and japonica parental lines and low outcrossing rates in the seed production process. Thus, the yield of seed production is low and unstable, which limits further application of indica-japonica hybrid rice. In this work, we review the influencing factors and genetic mechanisms of rice flowering habits. We also summarize and analyze the application research on these mechanisms in japonica CMS lines. This review provides a reference for promoting the breeding, production, and application of indica-japonica hybrid rice and the sustainable development of hybrid rice. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Progress in Molecular Genetic Research on Co-regulation of Grain Yield and Starch Quality in Rice LI Xingyi, CHEN Ling, SHAO Jiantao, XIAO Suqin, LI Jinlu, FU Huixian, YIN Fuyou, ZHANG Jianhong, CHENG Zaiquan, LIU Li Chinese Journal OF Rice Science    2026, 40 (1): 1-17.   DOI: 10.16819/j.1001-7216.2026.240901 Abstract （519）   HTML （25）    PDF （1773KB）（592）       Knowledge map    Save 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. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Cloning of Cold6 Conferring Cold Tolerance in Rice TAO Shibo, XU Na, XU Zhengjin, LIU Chang, XU Quan Chinese Journal OF Rice Science    2025, 39 (6): 751-759.   DOI: 10.16819/j.1001-7216.2025.240709 Abstract （488）   HTML （16）    PDF （1726KB）（930）       Knowledge map    Save 【Objective】 Exploring cold-tolerant germplasm and identifying cold-tolerant genes are essential strategies to mitigate cold stress in rice. 【Method】 We treated the japonica rice variety Sasanishiki with ethyl methanesulfonate (EMS) to select mutants exhibiting enhanced cold tolerance at the seed germination stage. Candidate genes underwent cloning and functional analysis using fine mapping, CRISPR/Cas9 gene editing, expression profiling, and haplotype analysis. 【Result】 We identified the mutant M34, which displayed markedly improved cold tolerance at the seed germination stage. Genetic analysis suggested that a single recessive gene governs this trait. Fine mapping pinpointed Cold6 as the target gene. CRISPR/Cas9-mediated knockout of Cold6 confirmed its role in regulating cold tolerance during germination. Cold6 expression was observed in all rice organs, peaking in the panicles, and it encodes a protein containing several functional domains, including SNF2. Evolutionary analysis indicated differentiation of Cold6 between indica and japonica varieties, with haplotype analysis revealing 10 distinct Cold6 haplotypes. The predominant haplotypes are I-III; haplotype I is prevalent in japonica rice, whereas II and III are common in indica rice. 【Conclusion】 This study identified Cold6 as a novel regulator of cold tolerance in rice at the seed germination stage, encoding an SNF2 protein. Investigating the molecular mechanism of Cold6 enhances our understanding of the SNF2 gene family's role in rice, offering a theoretical foundation and germplasm resources for breeding cold-tolerant, high-yield northern japonica rice. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Research Progress on Biological Functions of Ubiquitin-conjugating Enzymes in Rice WANG Juan, WU Lijuan, HONG Haibo, YAO Zhiwen, WANG Lei, E Zhiguo Chinese Journal OF Rice Science    2025, 39 (6): 744-750.   DOI: 10.16819/j.1001-7216.2025.250316 Abstract （486）   HTML （22）    PDF （794KB）（495）       Knowledge map    Save Ubiquitination is a critical post-translational modification, accounting for 80%-85% of protein degradation in eukaryotes. It regulates protein activity, localization, and function, thereby playing extensive roles in modulating diverse biological processes. The ubiquitin-conjugating enzyme E2, the second key enzyme in the ubiquitination cascade, acts not only as a ubiquitin carrier but also determines the type of ubiquitin linkages and the length of ubiquitin chains. A total of 48 E2 genes have been identified in rice, all encoding proteins that contain a highly conserved UBC (ubiquitin-conjugating) domain. This domain binds to ubiquitin via a thioester bond and forms a specific interaction interface with ubiquitin ligase E3, ensuring the precision of ubiquitin transfer. Studies have shown that E2 enzymes are widely involved in regulating rice growth and development, as well as responses to biotic stresses such as pathogen infection and abiotic stresses including drought and cold. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Quality Traits Affecting Eating Quality in indica Rice Under Different Nitrogen Application Levels in Early and Late Seasons in South China ZHANG Lanlan, LIU Dilin, MA Xiaozhi, HUO Xing, KONG Le, LI Jinhua, FU Chongyun, LIAO Yilong, ZHU Manshan, ZENG Xueqin, LIU Wuge, WANG Feng Chinese Journal OF Rice Science    2025, 39 (6): 832-846.   DOI: 10.16819/j.1001-7216.2025.240203 Abstract （470）   HTML （17）    PDF （2179KB）（445）       Knowledge map    Save 【Objective】 The taste of cooked rice is the most critical factor determining grain quality, which is influenced not only by the genetic background of variety but also by environmental factors such as fertilizer application rate and growing season. Systematically investigating the relationship between rice taste and other quality traits—including appearance, processing, cooking, and nutritional properties—under different nitrogen application levels and planting seasons can provide an important scientific reference for breeding new rice varieties with good taste under various production conditions. 【Method】 In 2021, 17 types of rice varieties (lines) from South China were used as test materials. Four nitrogen application treatments were applied: 0 kg/hm² (N0), 90 kg/hm² (N1), 135 kg/hm² (N2), and 180 kg/hm² (N3), in a field in both early and late seasons in Guangzhou City, Guangdong Province. Three-way ANOVA, stepwise multiple regression analysis, and path analysis were used to explore the relationship between rice taste and other major quality traits related to appearance, processing, cooking, and nutrition. 【Result】 The results showed that: (1) Chalky grain rate (CGR), chalkiness degree (CD), gel consistency (GC), and protein content (PC) were simultaneously influenced by seven factors: season, nitrogen application rate, variety, the interaction between growing season and nitrogen level, the interaction between season and variety, and the three-way interaction among growing season, nitrogen level and variety. These are the most unstable traits. In contrast, alkali spreading value (ASV) was significantly influenced only by growing season and variety, making it the most stable trait. The other six traits—brown rice rate (BRR), milled rice rate (MRR), length-to-width ratio (LWR), transparency (TR), and amylose content (AC)—exhibited moderate instability. (2) A total of 11 quality traits significantly affecting the taste value (TV) of cooked rice were identified across different nitrogen treatments in both early and late seasons. Among them, AC and PC were consistently detected in both seasons and in the comprehensive combined analysis, both exerting negative effects on TV. MRR, CGR, CD, TR and GC were repeatedly detected in the late season and in the combined analysis. BRR, head rice recovery (HRR), and ASV were only detected under the N0 treatment in the late season and in the combined analysis, respectively, while LWR was only identified in the combined analysis. (3) Among the 11 traits significantly influencing TV, only GC and LWR showed positive direct path coefficients and overall effects, indicating a positive regulatory role on TV. Although ASV and BRR exhibited positive direct path coefficients toward TV, their overall effects were negative, implying a net negative regulatory role. The other seven traits all functioned as negative regulators of TV. 【Conclusion】 Based on the magnitude and direction of the effects of these quality traits on TV, the target profile for developing new high-taste indica rice varieties should include: LWR ≥ 3.5, HRR ≥ 58%, TR = Grade 1, CGR ≤ 10%, CD ≤ 1%, AC = 13%-17%, ASV ≥ Grade 6.0, GC ≥ 60 mm, and PC of polished rice ≤ 6.4% Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Preliminary Analysis of Function and Mechanism of OsRDR5 Gene in Rice HOU Guihua, ZHOU Liguo, LEI Jianguo, CHEN Hong, NIE Yuanyuan Chinese Journal OF Rice Science    2025, 39 (6): 779-788.   DOI: 10.16819/j.1001-7216.2025.250208 Abstract （465）   HTML （19）    PDF （1908KB）（810）       Knowledge map    Save 【Objective】 Drought is a major constraint on rice production, and drought avoidance is the most important mechanism for drought resistance of crops. Understanding the mechanism of OsRDR5, a candidate gene of drought tolerance in rice, can provide a theoretical basis for the improvement of drought tolerance in rice.【Method】 The nucleotide sequence, protein domain and phylogenetic relationship of RDR5 were analyzed using the NCBI database. The tissue expression pattern was analyzed by qRT-PCR. An OsRDR5 gene knockout mutant was constructed by the CRISPR/Cas9 system. The effect of OsRDR5 on rice deep root ratio was evaluated by the "basket method".【Result】OsRDR5 has a Coa3_cc domain, belonging to the cytochrome c oxidase assembly factor 3 gene family. OsRDR5 is located in the endoplasmic reticulum and is expressed in roots, stems and leaves of rice. Phenotypic identification of deep root ratio showed that the wild type had a deep root ratio of 53.7%, while the mutant lines had a deep root ratio of 63.3% and 64.9%, respectively. The deep root ratio of the mutant was significantly increased. A total of 1434 differentially expressed genes were identified by root transcriptomic analysis. GO enrichment analysis revealed significant enrichment of these genes in pathways related to drought stress, including response to water deprivation, abscisic acid and reactive oxygen species, among which several NAC genes(OsNAC016, OsNAC45, etc.) related to drought stress were up-regulated in the water deprivation pathway.【Conclusion】OsRDR5 knockout affects the deep root ratio of rice and plays an important role in drought avoidance of rice. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Modifying Heading Date of Nanjing 46 via CRISPR/Cas9-mediated Genome Editing CHEN Wei, YE Yuanmei, ZHAO Jianhua, FENG Zhiming, CHEN Zongxiang, HU Keming, ZUO Shimin Chinese Journal OF Rice Science    2025, 39 (6): 760-770.   DOI: 10.16819/j.1001-7216.2025.240707 Abstract （438）   HTML （9）    PDF （2072KB）（1030）       Knowledge map    Save 【Objective】 Heading date is a key agronomic trait determining the regional and ecological adaptation of rice cultivars. We edited the heading date genes of the medium-maturing late japonica rice variety Nanjing 46 (NJ46) with excellent tasting to shorten its heading date thereby potentially expanding its planting area.【Method】 Using CRISPR/Cas9 technology, the editing constructs, pCAMBIA1305-Actin:Cas9-sgRNADTH8 and pCAMBIA1305-Actin:Cas9-sgRNAGhd2 targeting DTH8 and Ghd2, respectively, were developed and transformed into NJ46 via Agrobacterium-mediated transformation. Homozygous editing lines without exogenous components were screened and evaluated on heading date, agronomic traits and quality-related traits. 【Result】 Three homozygous mutant lines were obtained. The NJ46-dth8 lines (NJ46-dth8-1 to -3) presented 22-36 days earlier than NJ46 on heading date, while the NJ46-ghd2 lines (NJ46-ghd2-1 to -3) showed 14-15 days earlier. The heading date, major agronomic traits, and quality related components of the homozygous mutant lines were evaluated in different areas of central and northern regions of Jiangsu Province, and compared with the widely cultivated varieties Nanjing 9108 and Nanjing 518 in their respectively ecological zones. NJ46-ghd2-1 exhibited a significantly higher yield per plant than Nanjing 9108, while showing comparable heading date and quality traits, and performed better than the other two knockout lines. NJ46-dth8-1 showed no significant differences from Nanjing 518 in yield per plant and major quality traits, and performed better than the other two knockout lines.【Conclusion】 Knockout of DTH8 and Ghd2 genes in NJ46 yielded new germplasms suitable for planting in the northern and central region of Jiangsu Province, respectively, which will help expand the planting area of this excellent-tasting rice variety. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Regulation of Amylose Content in Rice by Editing Wx Using CBE Base Editor CHEN Yuye, JIAO Xiaozhen, WANG Jian, WANG Kejian, CHEN Feng, ZHU Keming, LIU Chaolei Chinese Journal OF Rice Science    2025, 39 (6): 771-778.   DOI: 10.16819/j.1001-7216.2025.240705 Abstract （434）   HTML （15）    PDF （1143KB）（861）       Knowledge map    Save 【Objective】 The Wx gene, a key regulator of amylose synthesis in rice, encodes a granule-bound starch synthase and plays a crucial role in determining the amylose content, thereby directly influencing the quality traits of rice. 【Method】 We used the CBE base editor to introduce base substitutions within the first exon of the Wx gene in Shendao18 variety, resulting in two distinct mutation types: GCCCCC→GCCCTT and GCCCCC→GCTCTC. Both mutations led to the substitution of proline with leucine at position 94 of the Wx protein, designated as WxP94L-1 and WxP94L-2 respectively. 【Result】 Field experiments demonstrated that compared to the wild type, both WxP94L-1 and WxP94L-2 plants exhibited no significant differences in plant height, tiller number per plant, panicle length, grain morphology or 1000-grain weight. Rice quality analysis revealed that the amylose content decreased from 14.9% (wild type) to 12.5% (WxP94L-1) and 12.1% (WxP94L-2), while traits such as viscosity, alkali spreading value and protein content showed no significant change compared to the wild type. 【Conclusion】 Our study successfully generated a novel allele of the Wx gene named WxP94L using CBE base editor which resulted in a slight reduction in amylose content; thus providing a way for enhancing rice quality. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Effect of Application Methods of Mixed Controlled-release Nitrogen Fertilizer on Yield and Nitrogen Utilization of Good Taste Quality japonica Rice Under Different Mechanical Transplanting Methods in the Huaibei Region BIAN Jinlong, REN Gaolei, QIU Shi, XU Fangfu, HU Zhonglei, ZHANG Hongcheng, WEI Haiyan Chinese Journal OF Rice Science    2025, 39 (6): 847-862.   DOI: 10.16819/j.1001-7216.2025.250811 Abstract （416）   HTML （19）    PDF （2521KB）（449）       Knowledge map    Save 【Objective】 This experiment was conducted to clarify the effects of application methods of mixed controlled-release nitrogen fertilizer on the yield and nitrogen utilization of good-eating quality japonica rice under different mechanical transplanting methods in Huaibei region, aiming to screen the optimal mixed controlled-release nitrogen fertilizer treatment that matches the nutrient absorption of good-eating quality japonica rice, and to provide a scientific basis for its high-yield, high-quality and simplified cultivation.【Method】 In this experiment, two good-eating quality japonica rice varieties, Xudao 9 and Nanjing 5718, were used as materials to study the effects on yield, population quality indices and characteristics of nitrogen absorption and utilization under different treatments. Controlled-release fertilizer and quick-acting nitrogen fertilizer were mixed at a ratio of 5:5. The controlled-release fertilizer was blended from fertilizers with four different release periods (40, 60, 80, and 100 d) at a ratio of 1:4 to form three mixing modes, designated as N1 (40+60), N2 (40+80), and N3 (40+100). Conventional urea split application (CK) was used as a control. 【Result】 (1) Under different mechanical transplanting methods, the N2 treatment achieved the highest yield. The increase in yield was mainly attributed to the significant increase in effective panicle number and total spikelet number. Under the wide-narrow row pot seedling mechanical transplanting method, the average yields of the N2 treatment over two years reached 11.29 t hm⁻² and 11.79 t hm⁻², showing significant increases of 6.01% and 6.89% compared with CK, respectively. Under the equal-row spacing blanket seedling mechanical transplanting method, the average yields of the N2 treatment over two years reached 10.71 t hm⁻² and 11.12 t hm⁻², showing significant increases of 5.05% and 5.30% compared with CK, respectively. (2) Under different mechanical transplanting methods, the average tiller number at maturity in the N2 treatment was significantly increased by 7.30%−10.44% compared with CK, which effectively promoted the formation of high-yield populations. Meanwhile, under the N2 treatment, the leaf area index and leaf photosynthetic potential during the heading-maturity stage were significantly increased by 3.47%−13.25% and 6.53%−7.77% compared with CK, respectively, effectively promoting the formation of high-photosynthetic-efficiency populations. (3) Under different transplanting methods, the partial factor productivity of applied nitrogen and the agronomic nitrogen use efficiency showed the order of N2 > N3 > CK > N1, while the nitrogen uptake efficiency and the nitrogen uptake per 100 kilograms of grain showed the order of N3 > N2 > CK > N1. In the N2 treatment, the partial factor productivity of applied nitrogen, agronomic nitrogen use efficiency, nitrogen uptake efficiency and nitrogen uptake per 100 kilograms of grain were 5.13%−6.44%, 12.74%-16.14%, 15.14%-16.62% and 2.35%-2.87% higher than those in CK, respectively. The higher nitrogen utilization rate led to greater dry matter accumulation in the population under the N2 treatment. Under the wide-narrow row pot seedling mechanical transplanting method, the average dry matter accumulation during the jointing-heading stage and the heading-maturity stage in the N2 treatment was higher than that in CK by 3.11% and 3.23%, and 6.85% and 11.62%, respectively, over the two years; under the equal-row spacing blanket seedling mechanical transplanting method, the average dry matter accumulation during the jointing-heading stage and the heading-maturity stage in the N2 treatment was higher than that in CK by 2.80% and 2.45%, and 5.61% and 9.23%, respectively, over the two years. 【Conclusion】 Under both wide-narrow row pot seedling mechanical transplanting and equal-row spacing blanket seedling mechanical transplanting methods, the one-time basal application of the N2 mixed controlled-release fertilizer best matched the nutrient absorption of good-eating quality japonica rice in the Huaibei region. It promoted the formation of high-yield and high-efficiency populations, and thus can be regarded as an effective measure for achieving increased yield and efficiency through simplified cultivation of good-eating quality japonica rice in the Huaibei region. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Identification of QTLs for Seed Storability in Dongxiang Wild Rice by Integrating BSA-Seq and QTL Analysis WANG Shilin, WU Ting, ZHOU Shiqi, SONG Siming, HU Biaolin Chinese Journal OF Rice Science    2025, 39 (6): 789-800.   DOI: 10.16819/j.1001-7216.2025.240807 Abstract （408）   HTML （16）    PDF （1690KB）（1521）       Knowledge map    Save 【Objective】 The storage of rice seeds is crucial for ensuring food security and supporting sustainable agricultural production. Mining more genetic resources associated with seed storability is conducive to laying a genetic foundation for developing new storage-tolerant varieties.【Method】 Using Dongxiang wild rice accession Dongye 80 as the donor and cultivated rice R974 as the recurrent parent, two sets of BC₃F₇ populations—backcross recombinant inbred lines (BILs) consisting of 364 lines and single-segment substitution lines (SSSLs) consisting of 84 lines—were constructed. Germination rates were recorded after artificial aging treatment. QTL mapping and BSA-seq analysis were integrated to identify QTLs for seed storability from Dongxiang wild rice. Candidate genes were further predicted using gene annotation, GO enrichment analysis, and gene sequencing.【Result】 A total of nine QTLs for seed storability were detected on chromosomes 1, 2, 3, 6, 7, 9, and 11 using SSSLs, designated qSS1.1, qSS1.2, qSS2.1, qSS2.2, qSS3, qSS6, qSS7, qSS9.1, and qSS11, with phenotypic variation explained (PVE) ranging from 1.60% to 17.82%. Seven of these QTLs carried favorable alleles from Dongye 80, among which qSS7 and qSS11 were novel. Meanwhile, BSA-seq analysis using BILs identified 37 genomic regions associated with seed storability on chromosomes 2, 4, 5, 6, 7, 8, 9, and 11. The qSS7 interval was consistently detected by both methods and was narrowed down to a 480.1 kb overlapping region. In addition, qSS4 and qSS9.2 were delimited to overlapping regions of 199.7 kb and 177.8 kb, respectively. By integrating annotation information, GO enrichment, and gene sequencing, LOC_Os04g31040 and LOC_Os04g31070, LOC_Os07g07930, and LOC_Os09g15800 and LOC_Os09g15835 were proposed as candidate genes for qSS4, qSS7, and qSS9.2, respectively.【Conclusion】 In this study, nine and 37 QTLs for seed storability were identified by QTL mapping and BSA-seq analysis, respectively. Candidate genes for qSS4, qSS7, and qSS9.2 were further inferred. Notably, the favorable alleles of qSS4 and qSS9.2 from Dongye 80 significantly enhanced seed storability. Analysis of the candidate genes for qSS4 and qSS9.2 provides a foundation for cloning seed storability genes from Dongxiang wild rice and utilizing them in genetic improvement of cultivated rice. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Research on Rice Lodging Resistance: Current Status, Challenges, and Future Directions LUO Xiaoyun, ZHENG Xingfei, PENG Xuanguo, YU Qizhi, DONG Hualin, YIN Desuo, WANG Hongbo, HU Jianlin, XUE Lian, HU Peng, XU Deze Chinese Journal OF Rice Science    2026, 40 (2): 181-195.   DOI: 10.16819/j.1001-7216.2026.240905 Abstract （407）   HTML （36）    PDF （1308KB）（1158）       Knowledge map    Save Lodging is a frequent issue in rice production and has been increasingly regarded as a crucial problem by crop researchers globally. This is because it leads to a substantial decline in both grain yield and quality. Drawing on research of domestic and international scholars in recent decades, this article reviews the concept, types, and detrimental effects of lodging in rice. It also examines the factors influencing the lodging resistance of rice and proposes corresponding countermeasures. Additionally, it summarizes the evaluation methods, genes and QTLs related to rice lodging resistance. Finally, this paper analyzes the existing problems and prospects for future research regarding rice lodging resistance, with the intention of offering valuable references for the breeding of rice varieties with enhanced lodging resistance. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Yield Formation and Photosynthetic Characteristics of Machine-transplanted Late-season Rice with Short Growth Duration LI Xing, ZHANG Ruichun, CHEN Ge, XIE Jiaxin, XIAO Zhengwu, CAO Fangbo, CHEN Jiana, HUANG Min Chinese Journal OF Rice Science    2025, 39 (6): 863-872.   DOI: 10.16819/j.1001-7216.2025.250106 Abstract （386）   HTML （15）    PDF （1399KB）（934）       Knowledge map    Save 【Objective】 This study aimed to investigate the high-yield formation and photosynthetic properties of early-season rice varieties used as short growth duration late-season rice under machine-transplanted conditions. The findings are expected to lay a theoretical basis for breeding short growth duration late-season rice varieties and promoting their large-area, high-yield cultivation. 【Method】 Field experiments were conducted from 2021 to 2023 in Yong'an Town, Liuyang City, Hunan Province. Two early-season varieties, Zhongjiazao 17 and Zhongzao 39, which show significant yield differences, were used as experimental materials. Their yield, yield components, dry matter accumulation, leaf photosynthetic characteristics, and canopy structure were measured when grown as short growth duration late-season rice under machine-transplanted conditions. 【Result】 Averaged over the three years, the yield of Zhongzao 39 was 19.76% higher than that of Zhongjiazao 17. In terms of yield components, the 1000-grain weight of Zhongzao 39 was significantly higher (by 7.60%) than that of Zhongjiazao 17. Regarding dry matter production, Zhongzao 39 accumulated 12.24% more of total dry matter than Zhongjiazao 17, mainly due to its stronger pre-heading dry matter production capacity. Zhongzao 39 exhibited stronger early vigor, superior leaf photosynthetic performance at heading, and a better canopy structure during the vegetative growth stage. Specifically, at the heading stage, its net photosynthetic rate, chlorophyll a and b contents, total chlorophyll content, leaf nitrogen content, and specific leaf weight were 10.38% to 29.04% higher than those of Zhongjiazao 17. Furthermore, canopy structure indicators—including pre-heading crop growth rate, leaf area duration, radiation use efficiency, and leaf area index at heading—were 17.80% to 25.95% higher in Zhongzao 39 than those in Zhongjiazao 17. 【Conclusion】 Under machine-transplanted conditions, short growth duration late-season rice varieties characterized by high 1000-grain weight, strong early vigor, and enhanced photosynthetic capacity at the heading stage demonstrate greater yield potential. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Advances in Molecular Mechanism and Breeding Application of Heading Date Regulation in Rice YANG Dabing, DU Xueshu, LI Jinbo, XIA Mingyuan, HU Liang, SHI Huan, WAN Bingliang Chinese Journal OF Rice Science    2026, 40 (2): 145-154.   DOI: 10.16819/j.1001-7216.2026.250706 Abstract （383）   HTML （30）    PDF （1085KB）（1281）       Knowledge map    Save Heading date, a pivotal agronomic trait determining rice production seasons and regional adaptability, is fundamental for breeding high-yield cultivars tailored to specific ecological environments. In recent years, numerous genes controlling heading date in rice have been cloned, and their functional mechanisms have been increasingly elucidated. Consequently, the molecular regulatory network governing heading date has become progressively refined. This review systematically summarizes the molecular mechanisms regulating rice heading date, with a focus on the photoperiodic regulatory network, and discusses its applications in breeding practices. It aims to provide a theoretical foundation for the genetic improvement of heading date and ecological adaptability breeding in rice. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Function of OsERF93 in Regulating Resistance to Sheath Blight in Rice YUE Xuanyu, XIE Wenya, FENG Zhiming, CHEN Zongxiang, HU Keming, ZUO Shimin Chinese Journal OF Rice Science    2026, 40 (1): 37-50.   DOI: 10.16819/j.1001-7216.2026.250202 Abstract （383）   HTML （18）    PDF （1731KB）（423）       Knowledge map    Save 【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. Table and Figures | Reference | Supplementary Material | Related Articles | Metrics | Comments（0）

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Effects of Application Time and Rate of Bud-promoting Fertilizer on Main Crop Quality and Annual Yield of Ratoon Rice XIAO Wuwei, ZHANG Yuqing, ZHU Chenguang, TIAN Guisheng, CAI Yuehong, WANG Fei, XIONG Dongliang, HUANG Jianliang, PENG Shaobing, CUI Kehui Chinese Journal OF Rice Science    2026, 40 (1): 118-130.   DOI: 10.16819/j.1001-7216.2026.241009 Abstract （383）   HTML （18）    PDF （1510KB）（481）       Knowledge map    Save 【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. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Identification of Genes for Rice Seed Storability and Transcriptome Analysis Under Different Aging Conditions LIAO Zhengming, GUO Liang, PAN Xiaowu, LI Yongchao, DONG Zheng, LI Xiaoxiang Chinese Journal OF Rice Science    2026, 40 (1): 95-105.   DOI: 10.16819/j.1001-7216.2026.241110 Abstract （369）   HTML （10）    PDF （2046KB）（408）       Knowledge map    Save 【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. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Assembly, Codon Usage Bias, and Phylogenetic Analysis of Chloroplast Genome of Oryza meyeriana LI Rongxin, WANG Bo, XIAO Suqin, YIN Fuyou, ZHANG Jianhong, ZHONG Qiaofang, CHEN Ling, LI Jinlu, YANG Hesheng, CHENG Zaiquan, LIU Li Chinese Journal OF Rice Science    2025, 39 (6): 801-812.   DOI: 10.16819/j.1001-7216.2025.240612 Abstract （361）   HTML （7）    PDF （2031KB）（2447）       Knowledge map    Save 【Objective】 Oryza meyeriana, which is shade-tolerant and retains many primitive traits, is the only xerophytic type of wild rice in the genus Oryza. This study aims to enrich the genetic foundation of O. meyeriana and provide reference for vector construction of its superior genes. 【Methods】 The chloroplast genome of Yunnan O. meyeriana was sequenced using second-generation sequencing technology, followed by assembly and annotation. Codon usage bias and phylogenetic relationships were analyzed with RStudio and MEGA. 【Results】 The results showed that the total length of the chloroplast genome was 135,937 bp, with a GC content of 39.0%. The average effective number of codons(ENC) value was 48.09, indicating weak codon usage bias. ENC-plot, PR2-plot, and neutral plot analyses revealed that selection pressure plays a major role in shaping the chloroplast codon usage bias in Oryza meyeriana, and that this bias mainly regulates genes involved in self-replication and the photosynthetic system. A total of 16 optimal codons were identified, among which 14 ended with A/U and 2 ended with G/C. Phylogenetic analysis based on the chloroplast genome showed that Oryza meyeriana is closely related to O. brachyantha.【Conclusion】 This study enriches our understanding of the genomic composition and genetic information of Oryza meyeriana. The findings provide a basis for mining favorable genes related to photosynthesis and for investigating the evolution of wild rice species. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Mapping Analysis of a New Bacterial Blight Resistance Gene Xa49(t) in Rice DENG Huan, LIU Yapei, WANG Chunlian, GUO Wei, CHEN Xifeng, JI Zhiyuan Chinese Journal OF Rice Science    2025, 39 (6): 825-831.   DOI: 10.16819/j.1001-7216.2025.240302 Abstract （343）   HTML （14）    PDF （1308KB）（479）       Knowledge map    Save 【Objective】 Bacterial blight (BB) is one of the most serious diseases in rice. Breeding and planting resistant varieties is the most efficient strategy for disease control, and exploring resistance (R) genes is key to developing BB-resistant varieties. 【Method】 Wild rice provides valuable genetic resources for rice breeding. In this study, an introgression line, W6023, derived from a cross between Oryza rufipogon and Oryza sativa (IR24), was used. Genetic and resistance spectrum analyses revealed that W6023 carries a novel dominant BB R gene, tentatively named Xa49(t). An F₂ segregating population from IR24 × W6023 was constructed, and bulk segregant analysis (BSA) combined with newly designed InDel and SNP markers was applied for preliminary mapping of the target gene Xa49(t). 【Result】 Thirteen molecular markers linked to Xa49(t) were identified on chromosome 11, and the gene was ultimately delimited to a region between markers D11-111 and D11-241. 【Conclusion】 The novel broad-spectrum BB R gene Xa49(t) was preliminarily mapped to an approximately 968 kb region on rice chromosome 11. Table and Figures | Reference | Related Articles | Metrics | Comments（0）

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Advances and Prospects in Breeding Bacterial Blight-resistant Rice in South China MIAO Zhening, CHEN Jijin, LI Ziming, LIU Yi, LUO Lijun Chinese Journal OF Rice Science    2026, 40 (1): 18-26.   DOI: 10.16819/j.1001-7216.2026.250113 Abstract （341）   HTML （17）    PDF （1101KB）（628）       Knowledge map    Save 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. Table and Figures | Reference | Related Articles | Metrics | Comments（0）