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10 September 2026, Volume 40 Issue 5 Previous Issue   
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Research Progress of Rice Breeding by Molecular Design TONG Yi, QIAN Qian, GAO Zhenyu 2026, 40(5): 569-583.  DOI: 10.16819/j.1001-7216.2026.251009 Abstract ( )   PDF (871KB) ( )   To date, crop breeding has gone through four main stages: domestication breeding, conventional breeding, molecular breeding, and breeding by molecular design. In recent years, with the cloning of important functional genes in rice and the development of gene editing technologies, breeding by molecular design has shown its advantages. This manuscript reviews the progress of breeding technologies and breeding by molecular design in rice, summarizes its theoretical basis and achievements, discusses some issues and makes prospects, aiming to provide an outlook for rice breeding and molecular design breeding in other crops in the future.

Research Papers

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Cloning and Haplotype Analysis of GSN4, a Gene for Grain Size and Grain Number in Rice CHAI Bingze, WANG Junge, WU Kaixiong, LIU Jialong, WU Yue, WANG Huisen, TAN Lin, REN Deyong1, GAO Zhenyu, ZHU Li, ZHANG Qiang, ZHANG Guangheng, QIAN Qian, HU Jiang 2026, 40(5): 584-597.  DOI: 10.16819/j.1001-7216.2026.251212 Abstract ( )   PDF (3281KB) ( )   【Objective】Grain size is a critical determinant of rice yield. This study aims to explore novel genes regulating grain size and expand the current genetic regulatory network, and provide valuable genetic resources for molecular design breeding of high-yield rice varieties.【Method】The large-grain mutant gsn4, generated by EMS mutagenesis of the japonica rice variety W7, was used as experimental material. A combination of systematic phenotypic identification, cytological observation, gene mapping, functional verification, subcellular localization, and haplotype analysis was performed to clone and functionally characterize the candidate gene.【Result】 Phenotypic identification revealed that the gsn4 mutant exhibited pleiotropic effects. Compared with the wild type, its grain length, grain width, and 1000-grain weight were significantly increased, whereas plant height, panicle length, and grain number per panicle were significantly decreased. Cytological analysis indicated that GSN4 regulates rice grain size by modulating both cell proliferation and expansion in glumes. Map-based cloning, together with CRISPR/Cas9 gene-editing validation, confirmed LOC_Os04g46450 as the candidate gene underlying GSN4. This gene encodes a nuclear-localized E3 ubiquitin ligase protein, which acts as a negative regulator of rice grain size and modulates plant growth and development through the brassinosteroid (BR) biosynthesis pathway. Haplotype analysis further identified Hap1 as the elite haplotype conferring the most favorable effects on grain width and 1000-grain weight. 【Conclusion】Collectively, this study elucidates the function and regulatory mechanism of GSN4, enriches the genetic regulatory network governing rice grain size, and provides important genetic resources and a theoretical basis for molecular design breeding of high-yield rice varieties.

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A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima LI Xiaoxia, ZHANG Tianchi, HE Wenchuang, HE Huiying, PAN Nan, LIU Yifan, QIAN Qian, SHANG Lianguang 2026, 40(5): 598-606.  DOI: 10.16819/j.1001-7216.2026.250213 Abstract ( )   PDF (828KB) ( )   【Objective】Transposable elements (TEs) are a significant source of genetic diversity in rice and play a crucial role in the domestication process of Asian cultivated rice. However, due to the highly repetitive nature of TE sequences, their identification typically requires high-quality genome sequences. Currently, the limited genomic resources for African cultivated rice (Oryza glaberrima, Og) hinder systematic investigations into TE diversity and its contributions to the Og domestication process.【Method】We constructed a high-resolution pan-TE variation map using the chromosome-level genomes of 21 accessions (11 Og and 10 Oryza barthii [Ob]). We estimated the divergence of each TE variation across the genome using FST analysis and identified 854 selected TE variations putatively involved in the Og domestication process.【Result】The pan-TE variation map comprises 17,097 non-redundant high-quality TE variations with a total length of 39.1 Mb, with 61.7% of the TE variations larger than 1 kb. The total number of TE variations in the Ob accessions was greater than that in the Og accessions. A total of 658 genes harboring selected TE variations were identified as potentially involved in the Og domestication process, which were significantly enriched in biological processes related to basic metabolism. Notably, 30 genes with known functions were involved in the independent domestication of Og.【Conclusion】This study highlights the significant role of TE variations as a source of phenotypic diversity during the Og domestication process. The high-quality pan-TE variation map not only enriches the available variation library for rice breeding but also provides critical theoretical foundations and resource support for the genetic improvement of Og germplasm.

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Map-based Cloning and Functional Characterization of AGL1, a Gene Regulating Lemma and Palea Development in Rice FENG Pulin, YANG Qiwen, WU Jiayi, FAN Mingqian, CHENG Yanshuang, QIU Zhonghua, GUO Ran, CHEN Wenfu, WANG Jiayu 2026, 40(5): 607-617.  DOI: 10.16819/j.1001-7216.2026.250909 Abstract ( )   PDF (2145KB) ( )   【Objective】Rice lemma and palea development directly affects grain shape, pollination efficiency, yield and quality. This study identified mutants related to rice glume development, mapped and cloned the causal genes, and elucidated the molecular mechanisms by which the target genes regulate glume development, providing theoretical references for rice molecular breeding. 【Methods】The agl1 mutant was obtained by EMS mutagenesis of japonica cultivar SN9816. Paraffin sectioning and scanning electron microscopy were used to observe the morphology of glumes and floral organs; pollen viability was assessed by I₂-KI staining. Map-based cloning delimited AGL1, candidate genes were sequenced, and conservation and diversity of the target gene were analyzed. A Foss grain analyzer was used to measure brown-rice quality parameters.【Results】Compared with the wild-type SN9816, agl1 showed more strongly curved lemmas with unchanged longitudinal length, inwardly sunken paleae, and significantly narrowed lemma and palea; the lemma almost completely enclosed the palea. agl1 displayed abnormal lodicules, enlarged pistils and disordered stamens. Pollen activity and seed-setting rate were reduced. AGL1 was fine-mapped to a 68.7-kb interval between Indel4 and Indel5 on chromosome 2. Sequencing seven ORFs in this region revealed a single-nucleotide mutation in LOC_Os02g56610, which encodes a DUF640-domain protein. The DUF640 family in rice harbors a conserved ALOG domain and diverse regulatory elements, suggesting roles in both floral morphogenesis and grain quality. Quality analysis showed increased brown-rice protein and free fatty acid content but decreased amylose and total starch content, leading to poorer eating quality. 【Conclusion】The AGL1 gene functions as a pivotal regulator of rice lemma and palea development and grain quality; its loss-of-function disrupts hull morphogenesis, compromises pollen viability, and likely perturbs the grain-filling process, resulting in the concomitant deterioration of both yield and grain quality.

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Effects of Increased Seedling Transplanting Density with Reduced Nitrogen Fertilizer Application Level on Grain Yield and Quality of Mid-maturing Late japonica Rice Under Rapeseed Straw Return YU Bingjie, WANG Haoyu, GE Yutong, CUI Gege, ZHANG Haipeng, WEI Haiyan, ZHANG Hongcheng, XU Fangfu 2026, 40(5): 618-631.  DOI: 10.16819/j.1001-7216.2026.251007 Abstract ( )   PDF (793KB) ( )   【Objective】To explore the effects of increased basic seedling number and reduced nitrogen application on rice yield and quality, providing a scientific basis for green and high-efficiency rice production in Southern Jiangsu Province.【Method】Using the mid-maturing late japonica cultivar Nanjing 46, a field experiment was conducted in a rice-rapeseed rotation system during 2023 and 2024. The experiment included two basic seedling number: D1 (conventional, 1.1×106 seedlings/hm2) and D2 (a 50% increase, 1.7×106 seedlings/hm2). These were factorially combined with three nitrogen fertilizer rates: N1 (conventional application level, 270 kg/hm2), N2 (15% reduction, 230 kg/hm2), and N3 (30% reduction, 190 kg/hm2). The investigation focused on the treatment effects on key agronomic traits: grain yield, dry matter accumulation, leaf area index, photosynthetic potential, and grain quality parameters.【Results】The treatment with conventional seedling density and a 15% nitrogen reduction in nitrogen application (1.1×106 seedlings/hm2, 230 kg/hm2) produced the highest yield, while the treatment with a 50% increase in seedling density and a 30% reduction in nitrogen fertilizer application (1.7×106 seedlings/hm2, 190 kg/hm2) achieved a comparable yield. Compared to the conventional treatment (1.1×106 seedlings/hm2, 270 kg/hm2), the treatment with a 50% increase seedling density and a 30% reduction in nitrogen fertilizer application increased two-year average yield by 1.53%. In terms of yield components, this primarily resulted from increased panicle number, seed-setting rate, and 1000-grain weight. Compared to the conventional treatment, the treatment with a 50% increase in seedling density and a 30% reduction in nitrogen fertilizer application resulted in an average increase of 7.48% in the leaf area index at the maturity stage over the two years, as well as average increases of 7.03% and 1.01% in photosynthetic potential and aboveground dry matter accumulation from the heading to maturity stages, respectively. Under the treatment, the brown rice rate, milled rice rate, and head rice rate decreased by an average of 4.07%, 4.51%, and 6.16% over the two years, respectively, while the appearance quality, cooking and eating quality, and starch pasting properties were significantly improved.【Conclusion】Under rapeseed straw incorporation, the treatment with a 50% increase in seedling planting density and a 30% reduction in nitrogen fertilizer application achieved coordinated improvement in both rice yield and quality by balancing vegetative and reproductive growth, optimizing population biomass production and distribution efficiency, and promoting heading stage-maturity stage dry matter accumulation.

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Effects of Drip Irrigation Combined with Different Nitrogen Form Management Practices on Rhizospheric Nitrogen Transformation Process and Yield Formation in Rice YANG Changnan, HE Zixin, TAN Yawen, ZHANG Xuezhi, ZHANG Yecheng, TIAN Haoran, WEI Changzhou, ZHANG Xinjiang 2026, 40(5): 632-647.  DOI: 10.16819/j.1001-7216.2026.251008 Abstract ( )   PDF (1133KB) ( )   【Objective】A field experiment was conducted in an arid region to investigate the effects of nitrogen form and drip irrigation placement on nitrogen transformation dynamics in rice rhizosphere and yield formation, aiming to address low nitrogen use efficiency in drip-irrigated rice and provide theoretical and technical support for improving nitrogen management in these systems. 【Method】A three-factor randomized complete block design was adopted. The experimental factors included nitrogen application methods under drip irrigation, i.e., surface drip irrigation (Su) and subsurface drip irrigation at a depth of 10 cm (Sh); nitrogen forms, including no nitrogen application (N0), nitrate nitrogen (NN, calcium nitrate), and ammonium nitrogen combined with a nitrification inhibitor (AN, ammonium sulfate + DMPP, where DMPP is a nitrification inhibitor); and rice cultivars, namely Liangxiang 3 (LX3) and Ningjing 48 (NJ48). The three factors were fully crossed, resulting in 12 treatment combinations with three replicates for each combination. We conducted a comparative analysis of the following parameters across the different treatment combinations: rhizosphere soil pH, NH₄⁺-N and NO₃⁻-N content, nitrification rate and denitrification potential, aboveground nitrogen accumulation, and yield components. 【Result】Dry matter accumulation, nitrogen accumulation, and yield differed significantly among the treatment combinations. Overall, the AN treatment outperformed the NN and N0 treatments, with the Sh+AN combination yielding the highest results.The rhizosphere soil pH was significantly lower in the AN treatment than in the NN treatment. At both the tillering and heading stages, the soil NH₄⁺-N content differed significantly among nitrogen forms, with the AN treatment being significantly higher than the N0 and NN treatments. The highest values were observed in the Sh+AN combination (LX3: 20.39 mg/kg; NJ48: 21.05 mg/kg). Similarly, soil NO₃⁻-N content varied significantly among nitrogen forms, with the NN treatment significantly exceeding the N0 and AN treatments. The Su+NN combination showed the highest levels (LX3: 61.71 mg/kg; NJ48: 59.97 mg/kg). The soil potential nitrification rate and denitrification potential were significantly higher in the NN treatment than in the N0 and AN treatments. While these rates were slightly higher under Su irrigation compared to Sh, the difference was not statistically significant. 【Conclusion】Shallow subsurface drip irrigation at 10 cm depth combined with ammonium nitrogen stabilization management (Sh + AN) better maintained NH₄⁺-N levels in the rice rhizosphere and suppressed nitrification-related nitrogen loss. Consequently, this practice enhanced nitrogen uptake and increased grain yield. Therefore, the Sh+AN strategy can be recommended as an optimized nitrogen and irrigation management practice for drip-irrigated rice in the arid region of Xinjiang, effectively balancing yield enhancement with the mitigation of nitrogen loss.

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Layered Straw Returning Coupled with Decomposing Agent Enhances Rice Yield by Regulating Soil Organic Carbon Transformation and Microbial Community Structure WANG Xinya, HE Zhuoting, LI Xiao, YOU Saiya, ZHU Lianfeng, KONG Yali, ZHU Chunquan, TIAN Wenhao, ZHANG Junhua, JIN Qianyu, CAO Xiaochuang 2026, 40(5): 648-662.  DOI: 10.16819/j.1001-7216.2026.250711 Abstract ( )   PDF (1868KB) ( )   【Objective】This study investigated the effects of straw layered returning combined with its decomposing agents on the transformation of soil organic carbon (C), activities of enzymes related to C metabolism, structure of microbial community, and rice yield, in order to provide a theoretical basis for organic fertilization of low-yield yellow paddy soil and rice yield improvement. 【Method】Eight treatments were designed, including no fertilization (CK), conventional fertilization (NPK), and layered straw application at 0 cm, 0-8 cm, and 8-18 cm depths (NPKSL0, NPKSL0-8, and NPKSL8-18), and layered straw application combined with decomposing agents at 0 cm, 0-8 cm, and 8-18 cm depths (NPKSML0, NPKSML0-8, and NPKSML8-18). The content of soil organic C components, activity of C metabolism-related enzymes, soil microbial community, rice yield and its yield components were investigated, and their dominant factors that affect rice yield and soil organic C were further explored.【Result】Compared with NPK and NPKSL0-8, NPKSL8-18 treatment significantly increased the content of soil easily oxidizable organic C, microbial biomass C, particulate organic C, activity of α-glucosidase and β-glucosidase, and the relative abundance of Acidobacteriota and Ascomycota. Compared with the single straw application, the coupling application of straw and decomposing agents further increased soil organic C, easily oxidizable organic C, particulate organic C, mineral-bound organic C, and the activity of β-glucosidase in the 0-8 cm and 8-18 cm layers. Under NPKSML8-18 treatment, the abundance of Chloroflexi group was the highest, while the groups of Rozellomycota, Anaeromyxobacter, and Nigrospora were the lowest. Compared with NPK, NPKSML0, NPKSML0-8, and NPKSML8-18 increased soil organic C and rice yield, with the increments of 27.38%-37.94% and 7.97%-23.14%, and their values were highest in the NPKSML8-18 treatment. Correlation analysis showed that soil organic C and rice yield were significantly and positively correlated with soil easily oxidizable organic C, microbial biomass C, mineral-bound organic C, particulate organic C, and the activities of β-1,4-xylanase, α-1,4-glucosidase, and β-1,4-glucosidase (P<0.05), but were negatively correlated with dissolved organic C, the bacterial Shannon index and the fungal richness index (P<0.01).【Conclusion】Deep application of straw coupled with decomposing agents (NPKSML8-18) increases soil organic C and rice yield, mainly by enhancing the content of soil easily oxidizable organic C, microbial biomass C, mineral-associated organic C, and particulate organic C, boosting the activities of β-1,4-xylanase, α-1,4-glucosidase, and β-1,4-glucosidase, and promoting the relative abundance of Chloroflexi involved in straw decomposition.

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Intelligent Recognition Method of Rice Growth Stage Based on Multimodal Fusion XU Yongwei, LIU Shuhua, FENG Zelin, LUO Ju, NI Zhaoxin, YANG Baojun, YAO Qing, LI Agen 2026, 40(5): 663-678.  DOI: 10.16819/j.1001-7216.2026.250703 Abstract ( )   PDF (4733KB) ( )   【Objective】The growth period of rice is an important reference indicator for irrigation, fertilization, and pest control measures in rice planting management. Researching an intelligent recognition method for rice growth period based on multimodal fusion, improving the accuracy of rice growth period recognition, is of great significance for optimizing rice planting management measures and increasing rice yield. 【Method】To address the vulnerability of RGB images to lighting, an H-color channel image is extracted, and a dual-branch rice growth stage image recognition model based on residual network and attention mechanism is established; Due to the influence of meteorological factors on the length of rice growth period, a rice growth period meteorological identification model based on three meteorological factors and a bidirectional long-short period network is established; Using decision trees for decision-level multimodal feature fusion, multiple models were trained and tested on a self-built rice growth period dataset.【Result】The improved rice growth period image recognition model achieved an accuracy of 84.25%, which is superior to traditional image recognition models such as ResNet50 and ConvNeXt. The multi-modality model based on images and meteorological achieved an accuracy of 87.66% in identifying 9 rice growth stages, which is superior to the single modality recognition model based on images and meteorology.【Conclusion】The multimodal recognition model based on image and meteorological fusion compensates for the shortcomings of single modal recognition methods. Compared with single modal recognition models, it has significantly improved the accuracy of identifying 9 rice growth stages.

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Distribution of Ten Bacterial Blight Resistance Genes in Rice Varieties from South China FENG Aiqing, ZHANG Yabo, ZHOU Jiyong, SU Jing, FENG Jinqi, CHEN Kailing, CHEN Bing, LIANG Meiling, ZHU Xiaoyuan, WANG Congying, CHEN Shen 2026, 40(5): 679-695.  DOI: 10.16819/j.1001-7216.2026.251004 Abstract ( )   PDF (1094KB) ( )   【Objective】This study aims to assess the distribution of cloned or mapped bacterial blight resistance genes (Xa1, Xa3, Xa4, xa5, Xa7, xa8, Xa10, xa13, Xa21, and Xa23) in newly developed and widely cultivated rice varieties in South China. It also evaluates the effectiveness of gene combinations in providing resistance. The findings provide a scientific basis for the rational deployment of bacterial blight-resistant rice genotypes and the application of these resistance genes in the region.【Method】Using functional markers for the 10 resistance genes, 887 newly developed rice varieties from South China and 25 major rice varieties from Guangdong Province (2023–2024) were screened for resistance genes to bacterial blight. The resistance of 887 newly developed rice varieties to Xanthomonas oryzae pv. oryzae (Xoo) was identified by artificial leaf-cutting and inoculating with the dominant pathogenic strains of Xoo in South China. The resistance of the 25 major varieties in Guangdong Province was assessed using 102 representative strains from 11 major pathogenic types collected in 2024.【Result】Of the 887 new rice varieties, the frequencies of varieties carrying Xa1, Xa23, Xa3, Xa7, Xa4, Xa21, and xa8 were 16.57%, 12.63%, 6.99%, 5.98%, 1.92%, 1.92%, and 0.34%, respectively, while no varieties carried xa5, Xa10, or xa13. Among the new varieties, 0.34% carried 4 resistance genes, 0.34% carried 3 genes, 6.99% carried 2 genes, 29.99% carried 1 gene, and 62.34% carried no resistance genes. Among the 68 new varieties with gene combinations, the most frequent genes were Xa23, Xa1, Xa3, Xa7, Xa4, and Xa21, with application frequencies of 63.23%, 63.23%, 38.23%, 27.94%, 14.71%, and 5.88%, respectively. Of the 887 varieties, 20.41% were resistant to the dominant Xoo pathogen in South China, while 79.59% were susceptible. The percentages of resistant varieties harboring only one of the genes Xa23, Xa4, xa8, Xa7, Xa21, Xa3, and Xa1 were 92.75%, 42.86%, 33.33%, 32.35%, 23.08%, 11.11%, and 7.69%, respectively. Among new varieties with 4, 3, 2, 1, and 0 resistance genes, the percentages of resistant varieties were 100%, 100%, 64.52%, 35.34%, and 7.41%, respectively. 65.22% of varieties with Xa23 were resistant or moderately resistant, and among the new varieties developed by pyramiding Xa23 with different genes, 79.07% were rated as resistant or above. Among the new varieties carrying Xa7, 61.76% showed moderate susceptibility or worse, and 90% of varieties with pyramided Xa7 and other genes exhibited similar susceptibility. For the 25 main rice varieties in Guangdong, only 20% contained one or two resistance genes. The frequencies of Xa7, Xa4, and Xa3 were 4%, 8%, and 12%, respectively, while no other resistance genes were detected. Only 4% of the main varieties carried two resistance genes. Most of the 25 varieties were susceptible to the representative strains from Guangdong's pathotypes, with resistance frequencies generally low. Only Guang 8 You 2168, carrying Xa4 and Xa3, exhibited a resistance frequency of 20%, while other varieties had resistance frequencies below 10%. 【Conclusion】Currently, most of the new and main rice varieties in South China lack bacterial blight resistance genes or effective gene combinations, leading to widespread susceptibility and an escalating threat from bacterial blight. However, resistance increases with the number of resistance genes. Breeding rice varieties with multiple resistance genes is a promising strategy to address the evolving virulence of bacterial blight. Xa23, Xa7, Xa4, xa8, Xa21, Xa3, and Xa1 contribute to enhancing resistance, with Xa23 and Xa7 standing out as particularly effective and widely applicable resistance genes for future breeding in South China.

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Effects of Temperature and Insecticides on the Biological Traits of Haplogonatopus oratorius MA Xiaohui, MAO Ting, GUO Li, XING Yanan, SHAO Lingyun, CHE Xiqing, LIU Yu, YU Shenzhou 2026, 40(5): 696-704.  DOI: 10.16819/j.1001-7216.2026.260104 Abstract ( )   PDF (661KB) ( )   【Objective】 In the northern rice-growing areas, Haplogonatopus oratorius is the dominant natural enemy species of Laodelphax striatellus among dryinid wasps. Its population dynamics are closely related to external environmental factors. This study aims to clarify the effects of temperature and pesticides on the main biological parameters of H. oratorius under laboratory conditions.【Method】 Five temperatures (12, 18, 24, 30, and 36 °C) were set to examine their effects on the predation, parasitism, and adult longevity of the parental generation of H. oratorius, as well as on the cocooning rate, emergence rate, female proportion, and developmental duration of its offspring. Additionally, the lethal effects of two concentrations of chlorantraniliprole, abamectin, and pymetrozine were tested on the main developmental stages (parasitized hosts, cocoons, and adults) of H. oratorius.【Result】 1) Under different temperature conditions, the highest predation rate of H. oratorius was 20.5% (at 18 and 24 °C), and it gradually decreased from 18 to 36 °C, with the lowest rate being 9.0% (at 12 °C). The highest parasitism rate was 30.5% (at 30 °C), which gradually increased from 12 to 30 °C, and the lowest rate was 12.0% (at 36 °C). Adult longevity was longest at 18 °C (21.7 days for females, 3.7 days for males) and the shortest at 36 °C (2.8 days for females, 1.3 days for males). The cocooning rate (85.7%), emergence rate (76.2%), and the female proportion (38.1%) of offspring were all highest at 24 °C, while no offspring survived at 36 °C. 2) When parasitized hosts (5 and 12 days post parasitism) were treated with the tested insecticides, the mortality caused by chlorantraniliprole ranged from 62.5% to 75%, whereas abamectin and pymetrozine both caused 100% mortality. For cocoons treated for 3 and 7 days, mortality ranged from 3.3% to 30.0% for all tested insecticides. For adult females and males, abamectin caused 48 h mortality of 73.3%–90.0%, while chlorantraniliprole and pymetrozine caused 48 h mortality of 36.7%–73.3%.【Conclusion】 The suitable temperature range for H. oratorius is 18–30 °C; survival rate decreases significantly at both low and high temperatures, and no survival was observed at 36 °C. The wasp shows relatively strong tolerance to insecticides during the cocoon stage.