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    Improving Semi-Dried Brown Rice Noodle Quality via Mixed Fermentation of Lactobacillus and Yeast
    Luo Lijuan, Cheng Zixuan, Qiao Fan, Xiong Gangping, Liu Jun, Huang Qingming, Li Jiangtao, Lin Qinlu, Liu Chun
    Rice Science    2024, 31 (5): 489-493.   DOI: 10.1016/j.rsci.2024.06.005
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    Efficient Breeding of Early-Maturing Rice Cultivar by Editing Hd6 via CRISPR/Cas9
    Chen Zhihui, Tao Yajun, Xu Yang, Wu Jingjing, Wang Fangquan, Li Wenqi, Jiang Yanjie, Fan Fangjun, Li Xia, Zhu Jianping, Zhu Qian-Hao, Yang Jie
    Rice Science    2024, 31 (6): 629-633.   DOI: 10.1016/j.rsci.2024.06.007
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    In vivo Haploid Induction via Parthenogenesis Gene ToPAR in Rice
    XIONG Jie, JI Yajie, YANG Shenlin, QIU Xianjin, QIAN Qian, WANG Kejian
    Rice Science   
    Accepted: 11 December 2024

    Bulked Segregant RNA-Seq Analysis of Pollinated Pistils Reveals Genes Influencing Spikelet Fertility in Rice
    Kanokwan Kaewmungkun, Keasinee Tongmark, Sriprapai Chakhonkaen, Numphet Sangarwut, Theerachai Thanananta, Amorntip Muangprom
    Rice Science    2024, 31 (5): 556-571.   DOI: 10.1016/j.rsci.2024.06.001
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    Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F5:6 generation plants derived from inter-subspecific crosses (Nipponbare × KDML105) with low (LS) and high seed-setting rates (HS), in which normal pollen fertility was observed. However, LS plants showed a reduced number of pollen grains adhering to the stigma and fewer pollen tubes reaching the ovules at 4‒5 h post-pollination, compared with HS plants. Bulked segregant RNA-Seq analysis of pollinated pistils from the HS and LS groups revealed 249 and 473 differentially expressed genes (DEGs), respectively. Kyoto Encyclopedia of Genes and Genomes analysis of the HS and LS- specific DEGs indicated enrichment in metabolic pathways, pentose and glucuronate interconversions, and flavonoid biosynthesis. Several of these DEGs exhibited co-expression with pollen development genes and formed extensive clusters of co-expression networks. Compared with LS pistils, enzyme genes controlling pectin degradation, such as OsPME35 and OsPLL9, showed similar expression patterns, with higher levels in HS pistils pre-pollination. Os02g0467600, similar to cinnamate 4-hydroxylase gene (CYP73), involved in flavonoid biosynthesis, displayed higher expression in HS pistils post-pollination. Our findings suggest that OsPME35, OsPLL9, and Os02g0467600 contribute to prezygotic isolation by potentially modifying the stigma cell wall (OsPME35 and OsPLL9) and controlling later processes such as pollen-stigma adhesion (Os02g0467600) genes. Furthermore, several DEGs specific to HS and LS were co-localized with QTLs and functional genes associated with spikelet fertility. These findings provide valuable insights for further research on rice spikelet fertility, ultimately contributing to the development of high-yielding rice varieties.

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    Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based Plant Height Dynamics for Breeding
    Hong Weiyuan, Li Ziqiu, Feng Xiangqian, Qin Jinhua, Wang Aidong, Jin Shichao, Wang Danying, Chen Song
    Rice Science    2024, 31 (5): 617-628.   DOI: 10.1016/j.rsci.2024.04.007
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    Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. Plant height (PH) dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle (UAV)-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading (IH) and full heading (FH), and panicle initiation (PI), and growth period after transplanting (GPAT) were collected during the rice growth stage. PHs were extracted using a digital surface model (DSM) and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest (RF), support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th (R2 = 0.934, RMSE = 0.056 m). The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features (CF) and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI (R2 = 0.834, RMSE = 4.344 d), IH (R2 = 0.877, RMSE = 2.721 d), and FH (R2 = 0.883, RMSE = 2.694 d). Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.

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    Biofilmed-PGPR: Next-Generation Bioinoculant for Plant Growth Promotion in Rice under Changing Climate
    Jeberlin Prabina Bright, Hemant S. Maheshwari, Sugitha Thangappan, Kahkashan Perveen, Najat A. Bukhari, Debasis Mitra, Riyaz Sayyed, Andrea Mastinu
    Rice Science    2025, 32 (1): 94-106.   DOI: 10.1016/j.rsci.2024.08.008
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    The exopolysaccharide matrix of diazotrophic cyanobacteria was used to integrate phosphorus (P) and potassium (K) solubilizing bacteria, enhancing the survival of plant growth-promoting rhizobacteria, and ultimately the survival of bacteria in the rhizosphere for better plant growth. A new biofilm-based formulation comprising the diazotrophic cyanobacteria Anabaena AMP2, P-solubilizing Bacillus megaterium var. phosphaticum PB1, and K-solubilizing Rhizobium pusense KRBKKM1 was tested for efficacy in rice. The growth medium with half-strength BG-11 medium supplemented with 3% glucose showed best for biofilm formation under in vitro conditions. Analysis of the methanolic extract of the cyanobacterial- bacterial biofilm (CBB) showed the activity of antioxidants, such as 2-methoxy phenol and pentadecane, which are proven to improve plant-microbe interactions and plant growth, respectively. Treatment of rice seeds with CBB extract at 100 mL/kg or 200 mL/kg showed significant enhancement in germination rate and seedling length. Therefore, a pot culture experiment with the CBB formulations was carried out, and different growth and yield parameters were recorded. Principal component analysis showed that plant growth, yield, soil dehydrogenase activity, and soil chlorophyll content were positively correlated with rice plants amended with vermiculite-based CBB at 2 kg/hm2 followed by a spray with aqueous CBB formulation at 5 mL/L at 15 and 30 d after rice transplanting grown with a 25% reduced level of nitrogen/phosphorus/potassium chemical fertilizers than the recommended dose. Further, Pearson correlation analysis showed that yield was positively correlated with soil dehydrogenase (r = 0.92**) and soil chlorophyll content (r = 0.96**). We concluded that CBB could be used as a novel biofilm-based bio-inoculant to increase rice productivity and crop fitness as a component in integrated nutrient management and sustainable organic farming strategies with reduced chemical fertilizers.

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    Progress on Molecular Mechanism of Heat Tolerance in Rice
    Fu Yiwei, Wu Jiayelu, Wu Mingming, Ye Shenghai, Zhai Rongrong, Ye Jing, Zhu Guofu, Yu Faming, Lu Yanting, Zhang Xiaoming
    Rice Science    2024, 31 (6): 673-687.   DOI: 10.1016/j.rsci.2024.07.001
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    Rice (Oryza sativa L.) is a major food crop in China, and its high and stable yield is crucial for ensuring food security in the country. However, over the past few years, extreme weather events induced by global climate change have impacted rice growth. For example, the effects of heat stress on rice quality and yield have been significant. Therefore, it is fundamental to conduct in-depth research on the heat-tolerance mechanisms of rice and to cultivate superior new thermotolerant rice varieties. This review summarizes the adverse effects of high temperatures on rice growth at various stages, the heat-tolerance mechanisms in rice, and the heat-tolerance genes and QTLs that have been identified in recent years. We also discuss strategies to enhance the heat tolerance of rice, offering new insights for rice breeding research.

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    Next Generation Nutrition: Genomic and Molecular Breeding Innovations for Iron and Zinc Biofortification in Rice
    Kunhikrishnan Hemalatha Dhanyalakshmi, Reshma Mohan, Sasmita Behera, Uday Chand Jha, Debashis Moharana, Ahalya Behera, Sini Thomas, Preman Rejitha Soumya, Rameswar Prasad Sah, Radha Beena
    Rice Science    2024, 31 (5): 526-544.   DOI: 10.1016/j.rsci.2024.04.008
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    Global efforts to address malnutrition and hidden hunger, particularly prevalent in low- and middle-income countries, have intensified, with a focus on enhancing the nutritional content of staple crops like rice. Despite serving as a staple for over half of the world’s population, rice falls short in meeting daily nutritional requirements, especially for iron (Fe) and zinc (Zn). Genetic resources, such as wild rice species and specific rice varieties, offer promising avenues for enhancing Fe and Zn content. Additionally, molecular breeding approaches have identified key genes and loci associated with Fe and Zn accumulation in rice grains. This review explores the genetic resources and molecular mechanisms underlying Fe and Zn accumulation in rice grains. The functional genomics involved in Fe uptake, transport, and distribution in rice plants have revealed key genes such as OsFRO1, OsIRT1, and OsNAS3. Similarly, genes associated with Zn uptake and translocation, including OsZIP11 and OsNRAMP1, have been identified. Transgenic approaches, leveraging transporter gene families and genome editing technologies, offer promising avenues for enhancing Fe and Zn content in rice grains. Moreover, strategies for reducing phytic acid (PA) content, a known inhibitor of mineral bioavailability, have been explored, including the identification of low-PA mutants and natural variants. The integration of genomic information, including whole-genome resequencing and pan-genome analyses, provides valuable insights into the genetic basis of micronutrient traits and facilitates targeted breeding efforts. Functional genomics studies have elucidated the molecular mechanisms underlying Fe uptake and translocation in rice. Furthermore, transgenic and genome editing techniques have shown promise in enhancing Fe and Zn content in rice grains through the manipulation of key transporter genes. Overall, the integration of multi-omics approaches holds significant promise for addressing global malnutrition and hidden hunger by enhancing the nutritional quality of rice, thereby contributing to improved food and nutritional security worldwide.

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    RISE Method Based on Rare Allele Infusion and Sanger Sequencing Estimation: A Simple, Cheap, and Efficient Method for Detecting Transgene Copy Number in Rice
    Liu Tingchang, Huang Lifang, Liu Peng, Cui Yanchun, Chen Caiyan, Mao Donghai
    Rice Science    2024, 31 (5): 499-502.   DOI: 10.1016/j.rsci.2024.05.001
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    Biochar Decreases Soil Cadmium (Cd) Availability and Regulates Expression Levels of Cd Uptake/Transport-Related Genes to Reduce Cd Translocation in Rice
    Wang Han, Huang Qina, Zhang Yan, Shao Guosheng, Hu Yijun, Xu Youxiang
    Rice Science    2024, 31 (5): 494-498.   DOI: 10.1016/j.rsci.2024.04.004
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    Development of Machine Vision-Based Algorithm for Counting and Discriminating Filled and Unfilled Paddy Rice in Overlapping Mode
    Mahdieh Hoseingholizadeh-Alashti, Davood Kalantari
    Rice Science    2024, 31 (5): 503-506.   DOI: 10.1016/j.rsci.2024.04.001
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    Mixture of Bacillus Amyloliquefaciens and Bacillus Pumilus Modulates Community Structures of Rice Rhizosphere Soil to Suppress Rice Seedling Blight
    Jiang Nan, Qiu Jiehua, Tian Dagang, Shi Huanbin, Liu Zhiquan, Wen Hui, Xie Shuwei, Chen Huizhe, Wu Meng, Kou Yanjun
    Rice Science    2025, 32 (1): 118-130.   DOI: 10.1016/j.rsci.2024.09.001
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    Rice seedling blight, caused by various fungi, including Fusarium oxysporum, poses a severe threat to rice production. As awareness grows regarding the environmental and safety hazards associated with the application of fungicides for managing rice seedling blight, there has been a shift in focus towards biological control agents. In this study, we isolated biocontrol bacteria from paddy fields that significantly inhibited the growth of F. oxysporum in vitro and identified the strains as Bacillus amyloliquefaciens T40 and Bacillus pumilus T208. Additionally, our findings indicated that the combined application of these Bacillus strains in soil was more effective in reducing the incidence of rice seedling blight than their individual use. Analysis of 16S and internal transcribed spacer rRNA gene sequencing data revealed that the mixture of the T40 and T208 strains exhibited the lowest average clustering coefficients, which were negatively correlated with the biomass of F. oxysporum-inoculated rice seedlings. Furthermore, this mixture led to higher stochastic assembly (average |βNTI| < 2) and reduced selection pressures on rice rhizosphere bacteria compared with individual strain applications. The mixture of the T40 and T208 strains also significantly increased the expression of defense-related genes. In conclusion, the mixture of the T40 and T208 strains effectively modulates microbial community structures, enhances microbial network stability, and boosts the resistance against rice seedling blight. Our study supports the development and utilization of biological resources for crop protection.

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    Rice Cultivation under Film Mulching Can Improve Soil Environment and Be Beneficial for Rice Production in China
    Zhang Youliang, Zhu Kaican, Tang Yongqi, Feng Shaoyuan
    Rice Science    2024, 31 (5): 545-555.   DOI: 10.1016/j.rsci.2024.06.009
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    Rice cultivation under film mulching is an integrated management technology that can conserve water, increase soil temperature, improve yield, and enhance water and nitrogen use efficiencies. Despite these advantages, the system does have its drawbacks, such as soil organic matter reduction and microplastic pollution, which impede the widespread adoption of film mulching cultivation in China. Nonetheless, the advent of degradable film, controlled-release fertilizer, organic fertilizer, and film mulching machinery is promoting the development of rice film mulching cultivation. This review outlines the impact of rice cultivation under film mulching on soil moisture, soil temperature, soil fertility, greenhouse gas emissions, weed control, and disease and pest management. It also elucidates the mechanism of changes in rice growth, yield and quality, water use efficiency, and nitrogen use efficiency. This paper incorporates a review of published research articles and discusses some uncertainties and shortcomings associated with rice cultivation under film mulching. Consequently, prospective research directions for the technology of rice film mulching cultivation are outlined, and recommendations for future research into rice cultivation under film mulching are proposed.

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    Molecular Evolution of Rice Blast Resistance Gene bsr-d1
    Li Wei, Zhang Mengchen, Yang Yaolong, Weng Lin, Hu Peisong, Wei Xinghua
    Rice Science    2024, 31 (6): 700-711.   DOI: 10.1016/j.rsci.2024.08.004
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    Rice blast, caused by the fungus Magnaporthe oryzae, reduces rice yields by 10% to 35%. Incorporating blast resistance genes into breeding programs is an effective strategy to combat this disease. Understanding the genetic variants that confer resistance is crucial to this strategy. The gene Bsr-d1 encodes a C2H2-like transcription factor, and its recessive allele confers broad-spectrum resistance against infections by various strains of M. oryzae. In this study, we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice accessions. Our results revealed that wild rice exhibited significantly higher nucleotide diversity, with polymorphic regions primarily concentrated in the promoter region, in contrast to indica and japonica rice varieties. The Bsr-d1 gene displayed significant differentiation between indica and japonica rice varieties, with the bsr-d1 resistance allele being unique to indica rice. Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula. Moreover, we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene. In summary, our study uncovering the origin and evolution of bsr-d1 will enhance our understanding of resistance gene variation and expedite the resistance breeding process.

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    Breeding for Heat Tolerant Aromatic Rice Varieties and Identification of Novel QTL Regions Associated with Heat Tolerance During Reproductive Phase by QTL-Seq
    Surangkana Chimthai, Sulaiman Cheabu, Wanchana Aesomnuk, Siriphat Ruengphayak, Siwaret Arikit, Apichart Vanavichit, Chanate Malumpong
    Rice Science    2025, 32 (1): 67-80.   DOI: 10.1016/j.rsci.2024.12.002
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    Extremely high temperatures resulting from climate change have become a major challenge for increasing rice production. Therefore, our objective was to develop heat-tolerant aromatic rice varieties using the pedigree method, focusing on selecting for seed-setting ability under extremely high temperatures along with the use of single nucleotide polymorphism/insertion and deletion (SNP/InDel) markers to improve aromatic properties and grain quality. Furthermore, the QTL-seq approach was utilized to identify QTLs for seed-setting rate in an F2 population subjected to heat stress. The candidate QTL regions were then aligned to confirm SNPs/InDels in synonymous F7 candidate heat-tolerant lines. The results revealed that four promising lines, namely 84-7-1-9, 84-7-1-10, 159-3-3-1, and 159-3-3-10, were classified as heat-tolerant with low amylose content. In addition, lines 84-7-1-9 and 84-7-1-10 were identified as aromatic rice encompassing the aroma gene (badh2). Regarding the QTL-seq results, the qSF2.1 region ranged from 311 051 to 3 929 422 bp on chromosome 2, was identified based on the highest contrasting SNP index between the heat-susceptible and tolerant bulks. The candidate genes within this region include two genes related to heat shock proteins, three genes associated with pollen fertility, and four genes involved in heat stress and other abiotic stress responses. These genes are proposed as potential candidates for heat tolerance and could serve as targets in rice breeding programs aimed at enhancing heat tolerance.

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    Immune Sensor Xa21 Regulates Bacterial Leaf Blight Infection in Seven Rice Cultivars from Myanmar
    Nay Chi Aye, Rizwana Begum Syed Nabi, Muhammad Shahid, Nkulu Kabange Rolly, Rupesh Tayade, Lee-Bong Choon, Adil Hussain, Byung-Wook Yun
    Rice Science    2024, 31 (6): 634-637.   DOI: 10.1016/j.rsci.2024.06.008
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    Appropriate Supply of Ammonium Nitrogen and Ammonium Nitrate Reduces Cadmium Content in Rice Seedlings by Inhibiting Cadmium Uptake and Transport
    Hu Yunchao, Yan Tiancai, Gao Zhenyu, Wang Tiankang, Lu Xueli, Yang Long, Shen Lan, Zhang Qiang, Hu Jiang, Ren Deyong, Zhang Guangheng, Zhu Li, Li Li, Zeng Dali, Qian Qian, Li Qing
    Rice Science    2024, 31 (5): 587-602.   DOI: 10.1016/j.rsci.2024.02.007
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    Reasonable nitrogen (N) application is a promising strategy for reducing crop cadmium (Cd) toxicity. However, the specific form of N and the required amount that affect Cd tolerance and accumulation in rice remain unclear. This study explored the influence of different N-fertilizer forms (NH4NO3, NH4Cl, and KNO3) and dosages on Cd tolerance and uptake in Cd-stressed N-sensitive and N-insensitive indica rice accessions. The results indicated that the Cd tolerance of N-sensitive indica accessions is more robust than that of N-insensitive ones. Furthermore, the shoot Cd content and Cd translocation rate in both N-sensitive and N-insensitive indica accessions decreased with an appropriate supply of NH4NO3 and NH4Cl, whereas they were comparable or slightly increased with increased KNO3. Unfortunately, we did not find significant and regular differences in Cd accumulation or translocation between N-sensitive and N-insensitive rice accessions. Consistent with the reduction of shoot Cd content, the addition of NH4NO3 and NH4Cl also inhibited the instantaneous root Cd2+ uptake. The expression changes of Cd transport-related genes under different N forms and dosages suggested that the decreased shoot Cd content, caused by the increased supply of NH4NO3 and NH4Cl, is likely achieved by reducing the transcription of OsNRAMP1 and OsIRT1. In summary, our findings reveal that an appropriate supply of NH4NO3 and NH4Cl could reduce Cd uptake and transport in rice seedlings, suggesting that rational N management could reduce the Cd risk in rice production.

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    Applying Boron Fertilizer at Different Growth Stages Promotes Boron Uptake and Productivity in Rice
    Sitthikorn Bodeerath, Jeeraporn Veeradittakit, Sansanee Jamjod, Chanakan Prom-U-Thai
    Rice Science    2024, 31 (6): 751-760.   DOI: 10.1016/j.rsci.2024.08.007
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    Boron (B) is an essential micronutrient for plant growth and yield. We investigated the optimal growth stage for B fertilizer application to improve rice production. The study was conducted using a 2 × 4 factorial design in a randomized complete block during the rainy season of 2022. We utilized two premium Thai rice varieties Khao Dawk Mali 105 (KDML105) and Pathum Thani 1 (PTT1), and four soil B fertilizer treatments: a control (no B application), B application at the tillering stage, B application at the flowering stage, and B application at both the tillering and flowering stages. The results showed that the application of B fertilizer at the flowering stage and at both the tillering and flowering stages increased grain yield of KDML105 by 25.0% and 34.0%, respectively. In contrast, the grain yield of PTT1 showed no response to B application. The increased grain yield of KDML105 was attributed to an increased number of panicles per plant and a higher filled grain rate, which was due to the elevated B concentration in all plant parts and the total B uptake, particularly when B was applied at the flowering and tillering stages. Notably, B application increased the fertilized grain rates and reduced the proportion of unfertilized grains, a phenomenon that corresponded with the increased B concentration across all plant parts. The total B uptake ranged from 5.11 to 15.85 mg/m2 in KDML105 and from 8.37 to 24.26 mg/m2 in PTT1, with the highest total B uptake observed when B was applied at both the tillering and flowering stages for both rice varieties.

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    Fluorescence Detection of Bacterial Pathogens in Rice by Recombinant Polymerase Amplification Based on Self-Heating Paper Chip
    Yang Ning, Fu Jiuju, Wang Aiying, Liu Shuhua, Chang Kangpeng, Song Wei, Tao Shoulong, Mao Hanping, Zhang Xiaodong, Xu Lijia
    Rice Science    2025, 32 (2): 131-136.   DOI: 10.1016/j.rsci.2025.01.001
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    Breeding Resilience: Exploring Lodging Resistance Mechanisms in Rice
    Durga Prasad Mullangie, Kalaimagal Thiyagarajan, Manonmani Swaminathan, Jagadeesan Ramalingam, Sritharan Natarajan, Senthilkumar Govindan
    Rice Science    2024, 31 (6): 659-672.   DOI: 10.1016/j.rsci.2024.08.002
    Abstract108)   HTML4)    PDF (6882KB)(191)       Save

    Lodging is more than just plants falling over; it incurs significant economic losses for farmers leading to a decrease in both yield and quality of the final produce. Human management practices, such as dense sowing, excessive nitrogen fertilizer applications, inappropriate sowing dates, and upland rice cultivation, exacerbate the risk of lodging in rice. While breeders have developed high-yielding rice varieties utilizing the sd1 gene, relying solely on this gene is insufficient to enhance lodging resistance. Identifying the traits that contribute to lodging resistance is crucial. Key factors include biochemical, anatomical, and morphological traits, such as the levels of lignin, cellulose, hemicellulose, silicon, and potassium, along with the number and area of vascular bundles and the thickness, diameter, and length of the culm. Moreover, markers associated with lodging-related genes, like SCM2, SCM3, SCM4, and prl4, can be utilized effectively in marker-assisted backcrossing to develop rice varieties with desirable culm traits. This literature review aims to aid rice breeders in addressing the issue of lodging by examining traits that influence lodging resistance, developing phenotyping strategies for these traits, identifying suitable instrumentation, exploring methods for screening lodging-resistant plants, understanding the mathematical relationships involved, and considering molecular breeding aspects for pyramiding genes related to lodging.

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