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10 September 2025, Volume 39 Issue 5 Previous Issue   
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Reviews and Special Topics

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Advances in Roles of Different Types of Histone Modifications in Responses of Rice to Abiotic Stresses HAO Wenqian, CAI Xingjing, YANG Haidong, WU Yuyang, TENG Xuan, XUE Chao, GONG Zhiyun 2025, 39(5): 575-585.  DOI: 10.16819/j.1001-7216.2025.250203 Abstract ( )   PDF (1172KB) ( )   As one of the most important food crops in the world, the yield and quality of rice are directly related to global food security. However, rice often faces various abiotic stresses during growth, such as salt stress, drought, low and high temperatures, which seriously compromise the growth, development and yield of rice. In recent years, epigenetics research, especially the role of histone modifications in regulating stress tolerance responses of rice, has attracted increasing attention. This review summarizes the latest research progress in histone modifications in abiotic stress responses in rice, to provide a theoretical basis for genetic improvement and stress resistance breeding of rice.

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Research Progress on Physiological and Ecological Mechanisms and Regulation Pathways of Yield, Quality and Stress Resistance Response in Perennial Rice LU Tingting, YAN Wenhui, SU Xinquan, ZENG Luohua, HUA Liqin, CHEN Jianghua, FENG Baohua, WANG Yuexing, HU Jiang, FU Guanfu 2025, 39(5): 586-600.  DOI: 10.16819/j.1001-7216.2025.241012 Abstract ( )   PDF (15789KB) ( )   Perennial rice, characterized by its "one planting, two or more harvests", has become a crucial component of sustainable agriculture. Significant progress has been made in understanding the physiological and ecological mechanisms and regulation pathways of perennial rice. This study aims to systematically review the current status, yield and quality formation characteristics, physiological and ecological characteristics, and molecular mechanisms of perennial rice, with an in-depth discussion on its response mechanisms to stress conditions. Finally, we summarize the cultivation patterns and regulation strategies of perennial rice, providing theoretical foundations and practical guidance for expanding its planting regions and enhancing the diversity of rice germplasm resources.

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Research Progress in Regulation of Anthocyanin Accumulation in Colored Rice WU Wanting, XU Qian, LIU Dantong, ZHU Changjin, DU Haotian, JU Haoran, HUO Zhongyang, DAI Qigen, LI Guohui, XU Ke 2025, 39(5): 601-614.  DOI: 10.16819/j.1001-7216.2025.241206 Abstract ( )   PDF (14754KB) ( )   Colored rice is rich in protein, amino acids, cellulose, and essential minerals for the human body. It also contains active substances such as anthocyanins, which have anti-aging, cancer prevention, and antiviral effects, making it widely valued by consumers. This review focuses on summarizing the nutritional and health value of colored rice, and summarizes the accumulation, biosynthesis, and regulation processes of anthocyanins in colored rice from the perspectives of physiological and molecular regulation, as well as the effects of cultivation conditions such as temperature, light, water, and fertilizer level on the accumulation of anthocyanins. Finally, future research directions for colored rice are discussed.

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Functional Study on Aluminum Tolerance of OsAlR1 Gene in Rice WANG Jingbo, SU Chang, FENG Jing, JIANG Sixu, XU Hai, CUI Zhibo, ZHAO Minghui 2025, 39(5): 615-623.  DOI: 10.16819/j.1001-7216.2025.240510 Abstract ( )   PDF (1429KB) ( )   【Objective】With the aggravation of soil acidification, aluminum (Al) toxicity in acidic soil seriously limits the growth and development of rice. Mining Al-tolerant gene resources, analyzing their molecular functions, and breeding Al-tolerant varieties can ensure rice yield in acidic soil. 【Method】CRISPR/Cas9 technology was used to construct knockout vectors. The overexpression vector was constructed by homologous recombination and Golden Gate seamless cloning. Transgenic materials were obtained by genetic transformation. Homozygous overexpression lines and knockout lines were screened for Al tolerance phenotype analysis and determination of reactive oxygen species (ROS) content and antioxidant enzyme activities.【Result】qRT-PCR results showed that OsAlR1 expression was induced by Al stress. Knockout of OsAlR1 affected root development in rice. After Al treatment, compared with the wild type, the osalr1-3 and osalr1-6 lines accumulated more Al³⁺ and ROS, while the OE-OsAlR1-5 and OE-OsAlR1-8 lines accumulated less Al³⁺ and ROS. Knockout of OsAlR1 led to decreased glutathione (GSH) content and superoxide dismutase (SOD) activity in roots. qRT-PCR results revealed that genes regulating the phenylpropanoid biosynthesis pathway (OsPAL7, OsHCT4, OsCCR18, Os02g0467600, PRX82, and Os06g0522300) showed significant expression changes in the knockout lines after Al treatment.【Conclusion】 OsAlR1 expression is induced by Al stress, and OsAlR1 alleviates ROS-mediated oxidative stress by increasing GSH content and SOD activity. OsAlR1 may affect Al tolerance in rice by regulating the phenylpropanoid biosynthesis pathway.

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Directed Improvement of Hybrid Rice Zhuoliangyou 1126 by Heavy Ion Beam Mutagenesis Based on M1TDS Targeted Screening Technology SHAO Ye, HU Yuanyi, PENG Yan, MAO Bigang, LIU Huimin, TANG Chanjuan, LEI Bin, TANG Li, YU Lixia3, LI Wenjian3, LUO Wuzhong1, 2, LUO Zhibin, YUAN Yuantao, LI Yaokui, ZHANG Dan, ZHOU Libin, BAI Lianyang, TANG Wenbang, ZHAO Bingran 2025, 39(5): 615-623.  DOI: 10.16819/j.1001-7216.2025.240106 Abstract ( )   PDF (2113KB) ( )   【Objective】Using the two-line hybrid rice Zhuoliangyou 1126 as the base variety, we aimed to rapidly develop upgraded varieties with traits such as low cadmium accumulation, fragrance, storage tolerance, submergence tolerance, and a low glycemic index.【Method】Zhuo 234S and Xiangnonghui 1126, the parental lines of Zhuoliangyou 1126, were mutagenized using heavy-ion beams. Chimeric mutants of the OsNRAMP5, OsBADH2, OsLOX3, OsPAO5, OsSSIIIa, and OsBEIIb genes were identified in the M1 generation via M1TDS technology. Mutations in the target genes were further detected and isolated in the M2 generation using Kompetitive Allele-Specific PCR (KASP) genotyping. Hybrid rice with low cadmium accumulation was developed by crossing parents carrying OsNRAMP5 mutations.【Results】A total of 13 chimeric mutants involving six target genes were identified in the M1 generation. Among these, seven were confirmed to carry homozygous or heterozygous mutations in the M2 generation. The cadmium content in OsNRAMP5 homozygous mutants was significantly lower than in the wild type, while the content of the aromatic compound 2-acetylpyrroline (2-AP) was significantly higher in OsBADH2 homozygous mutants. When the low-cadmium hybrid rice derived from OsNRAMP5-mutated parents was pot-grown in cadmium-contaminated soil (available Cd: 0.677 mg/kg, pH 5.6), the cadmium content in grains remained consistently below 0.05 mg/kg, compared to 0.91 mg/kg in the wild-type control.【Conclusion】The combination of heavy-ion beam mutagenesis and M1TDS technology enabled the rapid improvement of traits such as low cadmium accumulation in Zhuoliangyou 1126. This study provides a successful example and a general technical reference for transitioning from traditional mutagenesis breeding to directed mutagenesis breeding.

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Evaluation of SNP Loci for Rice Variety Authenticity Verification XU Qun, WANG Shan, YUAN Xiaoping, JIN Shiqiao, JIN Fang, HAO Wanjun, WU Xiaobi, FENG Yue, YU Hanyong, SUN Yanfei, YANG Yaolong, WEI Xinghua 2025, 39(5): 635-642.  DOI: 10.16819/j.1001-7216.2025.241114 Abstract ( )   PDF (1364KB) ( )   【Objective】 A highly discriminative combination of SNP loci is crucial for developing efficient, accurate, and cost-effective rice variety verification technologies, which can be widely applied in seed regulation, variety breeding and other fields.【Method】 This study established fingerprints for 1,383 inbred and 2,702 hybrid rice varieties using the 96 SNP panel from the agricultural industry standard, designated RGIsnp96.【Result】 The results demonstrated that RGIsnp96 exhibited high polymorphism and strong discriminative power for variety identification. For 1,387 inbred varieties, the heterozygous rate, average polymorphic information content (PIC), and average minor allele frequency (MAF) of SNPs in RGIsnp96 were 0.03, 0.30, and 0.27, respectively. For 2702 hybrid varieties, the corresponding values were 0.39, 0.30, and 0.29, respectively. The identification rates, represented by the proportion of distinguishable variety pairs, for inbred and hybrid rice varieties were 99.94% and 99.99%, respectively. A good equivalence between RGIsnp96 and 48 SSRs in agricultural industry standards (designated RGIssr48 in the following) was evaluated by comparing similarities of variety pairs measured by the two marker sets for both inbred and hybrid varieties. Furthermore, combining RGIsnp96 and RGIssr48, representing different types of markers, could generate better results than using a single type of marker for differentiating certain inbred rice varieties, and corresponding strategies were recommended.【Conclusion】 RGIsnp96 demonstrates exceptional capability in rice variety identification, providing robust technical support for improving rice seed quality, regulating the seed market order, and safeguarding farmers' rights and interests.

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Creating a Fragrant Environment-insensitive Recessive Genic Male Sterile Germplasm Lacking Coleoptile Purple Lines by CRISPR/Cas9 Gene Editing YANG Jiaxin, GUAN Yusheng, DU Run, LI Xianyong, CAI Zuokun, WANG Chutao, YANG Qiyang, HE Yongxin, ZHU Zichao, ZHANG Yi 2025, 39(5): 643-649.  DOI: 10.16819/j.1001-7216.2025.240501 Abstract ( )   PDF (1119KB) ( )   【Objective】Hybrid rice has developed into the third generation in which environment-insensitive recessive genic male sterility (EI-RGMS) is the essential trait. In many rice breeding programs, fragrance improvement is an important target. Additionally, the purple line in coleoptile is a clearly identifiable anthocyanin trait at the very early germination stage, which facilitates simple, rapid, and accurate identification of hybrid purity. The purpose of this study is to develop a fragrant EI-RGMS material lacking the coleoptile purple line based on maintainer II-32B, providing a new core germplasm for the third-generation hybrid rice.【Methods】 Using CRISPR/Cas9, we knocked out the pollen development gene OsbHLH141, fragrance gene OsBadh2, and coleoptile purple line gene OsMYB76 in the elite rice parent II-32B.【Results】 Mutant lines with all three genes knocked out showed loss of anthocyanin traits, a distinct aroma, and male sterility.【Conclusion】 This study successfully created a fragrant EI-RGMS germplasm without purple line in coleoptile in the II-32B background.

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Effects of Nano-molybdenum on Root Morpho-physiological Traits and Nitrate Uptake in Rice ZHANG Haipeng, LI Wanyi, LIAO Fuxing, MA Meizi, ZHANG Hongcheng, YANG Yanju 2025, 39(5): 650-664.  DOI: 10.16819/j.1001-7216.2025.241006 Abstract ( )   PDF (1467KB) ( )   【Objective】Molybdenum (Mo) serves as an essential active component of nitrate reductase, playing a pivotal role in the reduction of nitrate nitrogen and nitrogen metabolism. This study aims to investigate the relationship between nano-MoO₃ and rice root morphology, organic acid secretion, and nitrate absorption, laying a theoretical basis for improving nitrate nitrogen absorption and utilization in rice through novel nano-fertilizers. 【Method】Using Nanjing 9108 rice as the research material, hydroponic experiments with nitrate nitrogen as the nitrogen source were conducted with treatments of no Mo application (Mo concentration, 0 μg/L), sodium molybdate (50, 100, 200, 400 μg/L), and nano-MoO₃ (50, 100, 200, 400 μg/L). Differences in rice root morphology, root-secreted organic acid, and nitrogen content were analyzed. 【Results】Exogenous Mo significantly increased rice root dry weight, total root length, root volume, total root surface area, total absorption area, and active absorption area, significantly optimizing rice root morphology compared to the no Mo treatment. At the same Mo application rates, nano-MoO₃ treatments showed significantly higher enhancement effects than sodium molybdate treatments. Root oxidation and reduction capacities, as well as organic acid secretion, increased significantly in response to exogenous Mo treatments, indicating enhanced root physiological activity. As Mo concentrations increased, the root oxidation and reduction capacities under sodium molybdate treatments initially increased and then decreased. Except for acetic acid, there were no differences in the secretion of malic acid, tartaric acid, succinic acid, citric acid, and oxalic acid at various sodium molybdate concentrations. However, both root oxidation/reduction capacities and organic acid secretion in nano-MoO₃ treatments increased with rising application rates. Factor analysis and redundancy analysis results indicated that rice root morphological indicators, root redox capacities, and organic acid secretion were positively correlated with root nitrogen content. Exogenous Mo addition promoted nitrate nitrogen absorption by rice roots through improvements in root morphological and physiological traits. 【Conclusion】Exogenous Mo enhanced rice root morphological and physiological activities by increasing root length, root surface area, redox capacities, and organic acid secretion, thereby promoting nitrate nitrogen absorption. Nano-MoO₃ demonstrated superior promotional effects compared to sodium molybdate at the same Mo application rates. In agricultural production, appropriate Mo fertilizer addition, especially nano-MoO₃ fertilizer, can improve rice root morphological and physiological functions, enhancing nitrate nitrogen absorption and utilization.

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Effects of Reducing Hill Density While Maintaining Plant Population on Dry Matter Accumulation and Transport in Rice Stem and Sheath Under Different Light Conditions LIU Yuting, ZHOU Xing, HE Chenyan, LI Qiuping, AI Xiaofeng, YUAN Yujie, LIU Rui, YANG Jingwen, LIU Tingting1, WANG Li, CHENG Hong, HUANG Rong, LI Aoyun, HU Wen, HU Zhong, REN Wanjun, DENG Fei 2025, 39(5): 665-678.  DOI: 10.16819/j.1001-7216.2025.240904 Abstract ( )   PDF (1636KB) ( )   【Objective】To clarify the effect of field configuration on dry matter accumulation and transport of culm and sheath under low light stress, and to provide a theoretical and practical basis for improving optimum canopy establishment technology in low light rice growing areas【Methods】 Using Yixiangyou 2115 as the material, experiments with different light conditions (natural light and 50% shading) and field configurations [conventional dense planting(CDP) and reducing hill density while maintaining plant population (RHMPP)] were conducted in Hanyuan County and Wenjiang District of Sichuan Province from 2021 to 2022. The effects of field configuration on dry matter accumulation and transport in rice internodes and leaf sheaths under different light conditions were studied.【Results】(1) Except for the Wenjiang site in 2022, low light stress significantly reduced the dry matter weight of individual internode and leaf sheath at maturity, which in turn significantly decreased the total dry matter weight of internodes and leaf sheaths by 22.68%−30.12% and 6.45%−15.64%, respectively, but significantly increased their total dry matter transport amount, transport rate, and contribution rate. (2) Compared with CDP, RHMPP could effectively increase the total dry matter weight of internodes(except at Wenjiang site under low light stress in 2022) and leaf sheaths during different growth stages under different light conditions, and promote the transport and reutilization of dry matter in internodes and leaf sheaths under low light stress, resulting in a 1.51%−6.03% and 5.70%−10.37% increase in single-panicle weight at maturity at Wenjiang and Hanyuan sites, respectively. (3) Under different light conditions, the correlation between grain yield, quality and dry matter accumulation and transport characteristics differed significantly. Under low light stress, the dry matter transport amount, transport rate, and contribution rate of internodes were positively correlated with grain yield, but highly significantly negatively correlated with the chalky grain rate and chalkiness degree. 【Conclusion】Under low light stress, rice maintains assimilate supply to panicles by enhancing the transport and reuse of culm and sheath, especially the dry matter of internodes. RHMPP, by improving pre-heading dry matter accumulation in the internodes and leaves promotes their transport thereby reducing the adverse effects of low light stress on rice yield and quality.

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Effect of Low Temperature at Booting Stage on Photosynthetic System of Different Rice Materials in Cold Region DING Guohua, LI Xin, CAO Liangzi, ZHOU Jinsong, LEI Lei, BAI Liangming, LUO Yu, YANG Guang, CUI Zhibo, ZHAO Minghui, SUN Shichen 2025, 39(5): 679-689.  DOI: 10.16819/j.1001-7216.2025.241014 Abstract ( )   PDF (2029KB) ( )   【Objective】The study aims to analyze the reasons for differences in photosynthetic system response to low temperature of early maturing rice materials at booting stage in cold regions, and to provide theoretical and material basis for breeding cold-tolerant and high-yield rice varieties at booting stage.【Method】 Using high-quality cold-tolerant variety Longdao 18 (LD18) and the new cold-sensitive high-yielding germplasm Longdao 17029 (L9) derived from crosses between LD18 and upland rice as experimental materials, we studied the effects of chilling injury on flag leaf chloroplast ultrastructure, photosynthetic parameters, related enzyme activities, and gene expression in materials with different cold tolerance.【Result】 Genomic analysis showed 75.03% similarity between LD18 and L9, with major differences on chromosomes 2 and 5. Under low temperature during booting-stage, LD18 had a significantly lower unfilled grain rate than L9. The SPAD value and chloroplast ultrastructure of LD18 flag leaves showed no significant changes, while L9 exhibited significantly decreased SPAD value, swollen and distorted chloroplasts and thylakoids, and produced abundant osmiophilic granules. Photosynthetic-related enzyme activities were higher in LD18 than those in L9. Transcriptomic and RT-qPCR results indicated more differentially expressed genes in LD18 than in L9. GO and KEGG analyses revealed that the most enriched pathways in LD18 versus L9 included photosynthesis and chlorophyll metabolism. RT-qPCR showed 3-fold upregulation of the photosynthesis-related gene RBCX1 in LD18 but downregulation in L9.【Conclusion】At booting stage under low temperature, LD18 exhibits stronger cold tolerance than L9. LD18 can mobilize more genes to cope with low-temperature stress, maintain chloroplast structural integrity, avoid reduction in chlorophyll content and photosynthetic rate, and maintain higher photosynthetic enzyme activities.

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Fertilization Effects of Different Exogenous Organic Materials in Newly Reclaimed Cultivated Land and Its Optimization of Evaluation Indicators YOU Saiya, WANG Xinya, QIN Birong, CAI Wenyan, ZHU Lianfeng, KONG Yali, ZHU Chunquan, TIAN Wenhao, ZHANG Junhua, JIN Qianyu, CAO Xiaochuang 2025, 39(5): 690-702.  DOI: 10.16819/j.1001-7216.2025.240720 Abstract ( )   PDF (1324KB) ( )   【Objective】The effects of different exogenous organic materials on soil fertility improvement in newly reclaimed hilly red soil and yellow clayey soil, as well as their minimum data set (MDS) based on the soil quality index (SQI), were investigated to provide theoretical and technical support for soil fertility cultivation in newly reclaimed farmland. 【Method】The experiment included seven fertilization treatments: no fertilizer (CK), chemical fertilizers (NPK) + 2250 kg/hm² straw (NPKS1), NPK + 4500 kg/hm² straw (NPKS2), NPK + 3000 kg/hm² decomposed straw-livestock manure (NPKSM), NPK + 1773 kg/hm² woody peat (NPKW1), and NPK + 3546 kg/hm² woody peat (NPKW2). Parameters including rice yield, soil aggregate structure, various forms of carbon and nitrogen, microbial biomass carbon and nitrogen, and enzyme activities were measured. The MDS for soil quality evaluation was selected, and the evaluation indicators were further optimized and validated.【Results】1) Compared with NPK, NPKSM significantly increased the proportion of large soil aggregates, mean weight diameter, soil organic matter, carbon-to-nitrogen ratio, and activities of soil enzymes (β-1,4-glucosidase (BG) and [β-1,4-N-acetylglucosaminidase (NAG)] in the hilly red soil. In the yellow clayey soil, NPKS2 significantly increased the contents of easily oxidizable organic carbon, mineral-associated organic carbon, and microbial biomass carbon and nitrogen, while NPKW2 significantly increased the contents of soil organic matter, particulate organic carbon, mineral-associated organic carbon, and dissolved organic carbon. 2) Principal component analysis showed that the mean weight diameter, ammonium nitrogen, and mineral-associated organic carbon constituted the MDS for soil quality evaluation in the hilly red soil, while the MDS for the yellow clayey soil consisted of the soil carbon-to-nitrogen ratio, mineral-associated organic carbon, and NAG activity. 3) SQI evaluation based on the total data set (TDS) and MDS indicated that the SQI of NPKSM in the hilly red soil, and of NPKS2 and NPKW2 in the yellow clayey soil, were significantly higher than those of the other treatments. 4)Regression analysis showed that the SQI evaluated based on the TDS and MDS were significantly and positively correlated in both soil types, demonstrating that the MDS can serve as an effective indicator for evaluating the fertilization effects of different organic materials.【Conclusion】The fertilization effects and evaluation indicators varied significantly among fertilization modes and soil types. The application of decomposed straw-livestock manure improved the SQI of the hilly red soil by significantly increasing organic matter, easily oxidizable organic carbon content, enzyme activities (BG and NAG), and aggregate stability, while woody peat enhanced soil quality mainly by increasing organic matter and mineral-associated organic carbon in the yellow clayey soil. In conclusion, the application of 3000 kg/hm² decomposed straw-livestock manure and 3546 kg/hm² woody peat can be recommended as suitable organic fertilization practices for newly reclaimed hilly red soil and yellow clayey soil, respectively.

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Effects of Exogenous miR3979 on Chemotaxis, Infection and Development of Root Knot Nematode Meloidogyne graminicola in Rice YANG Xingzhou, CUI Miaomiao, WEI Lihui, GU Aiguo, LI Dongxia, LE Xiuhu, FENG Hui 2025, 39(5): 703-710.  DOI: 10.16819/j.1001-7216.2025.240906 Abstract ( )   PDF (1263KB) ( )   【Objective】 miR3979-3p is involved in rice responses to multiple biotic and abiotic stresses. Its expression is downregulated in root tissues infected by the root-knot nematode Meloidogyne graminicola. Therefore, it is important to investigate the role of miR3979-3p in the interaction between M. graminicola and rice.【Method】 Rice roots were treated with artificially synthesized double-stranded miR3979 (ds-miR3979) via root soaking. Endogenous miR3979-3p expression levels were quantified using qPCR. Chemotaxis and infectivity of second-stage juveniles (J2s) were assessed through plate inoculation and tissue staining. The effects of ds-miR3979 treatment on root gall formation and nematode development were evaluated using pot inoculation assays.【Result】 Treatment with 100–800 nmol/L ds-miR3979 for 12–24 h had no significant effect on J2 motility. Compared with ddH₂O-treated controls, root soaking with 400 nmol/L ds-miR3979 for 12–24 h significantly upregulated miR3979-3p expression in both roots and leaves of rice seedlings at the seedling emergence and three-leaf stages. Continuous microscopic observation revealed reduced chemotactic movement of J2s toward root tips within 2–8 h, with significantly fewer nematodes aggregating around root tips. Plate inoculation showed a decrease in the number of nematodes penetrating roots at 1–3 days post-inoculation (dpi). Pot inoculation assays demonstrated significant reductions in root gall number, number of females within roots, and proportion of females at 7–21 dpi, along with delayed female development.【Conclusion】 Artificially synthesized ds-miR3979 can be taken up by rice plants, upregulating endogenous miR3979-3p expression, thereby inhibiting M. graminicola infection and female development.