Pub Date : 2025-03-01DOI: 10.1016/j.rsci.2024.12.012
Wang Shuman , Zhang Linqi , Gao Ruiren , Wei Guangbo , Dong Weiguo , Xu Jiming , Wang Zhiye
CRISPR-Cas endonucleases mediate prokaryotic adaptive immunity by targeting foreign nucleic acids. CRISPR/Cas13b is a class 2 type VI-B ribonuclease that targets and cleaves single-stranded RNA. It exhibits higher RNA interference activity than Cas13a and Cas13c and causes fewer collateral effects than RxCas13d in mammalian cells. However, a programmable CRISPR/Cas13b-mediated RNA interference system for endogenous transcripts in rice has not yet been established. Here, we developed a CRISPR/Cas13b-mediated system to target endogenous transcripts in rice. Our CRISPR/Cas13b system could inhibit multiple endogenous mRNAs simultaneously. In addition, this system efficiently repressed endogenous long noncoding RNAs with more than 50% inhibition in stable transgenic plants. Furthermore, we found only weak collateral effects of the CRISPR/Cas13b-mediated system at the transcriptome-wide level, and no difference in the agronomic traits of stable transgenic rice in the field. We present a programmable CRISPR/Cas13b-mediated knockdown system for rice, offering a potential biotechnological tool for functional genomics and crop improvement.
{"title":"Establishing Programmable CRISPR/Cas13b-Mediated Knockdown System in Rice","authors":"Wang Shuman , Zhang Linqi , Gao Ruiren , Wei Guangbo , Dong Weiguo , Xu Jiming , Wang Zhiye","doi":"10.1016/j.rsci.2024.12.012","DOIUrl":"10.1016/j.rsci.2024.12.012","url":null,"abstract":"<div><div>CRISPR-Cas endonucleases mediate prokaryotic adaptive immunity by targeting foreign nucleic acids. CRISPR/Cas13b is a class 2 type VI-B ribonuclease that targets and cleaves single-stranded RNA. It exhibits higher RNA interference activity than Cas13a and Cas13c and causes fewer collateral effects than RxCas13d in mammalian cells. However, a programmable CRISPR/Cas13b-mediated RNA interference system for endogenous transcripts in rice has not yet been established. Here, we developed a CRISPR/Cas13b-mediated system to target endogenous transcripts in rice. Our CRISPR/Cas13b system could inhibit multiple endogenous mRNAs simultaneously. In addition, this system efficiently repressed endogenous long noncoding RNAs with more than 50% inhibition in stable transgenic plants. Furthermore, we found only weak collateral effects of the CRISPR/Cas13b-mediated system at the transcriptome-wide level, and no difference in the agronomic traits of stable transgenic rice in the field. We present a programmable CRISPR/Cas13b-mediated knockdown system for rice, offering a potential biotechnological tool for functional genomics and crop improvement.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"32 2","pages":"Pages 217-227"},"PeriodicalIF":5.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-01DOI: 10.1016/j.rsci.2025.01.001
Ning Yang , Jiuju Fu , Aiying Wang , Shuhua Liu , Kangpeng Chang , Wei Song , Shoulong Tao , Hanping Mao , Xiaodong Zhang , Lijia Xu
{"title":"Fluorescence Detection of Bacterial Pathogens in Rice by Recombinant Polymerase Amplification Based on Self-Heating Paper Chip","authors":"Ning Yang , Jiuju Fu , Aiying Wang , Shuhua Liu , Kangpeng Chang , Wei Song , Shoulong Tao , Hanping Mao , Xiaodong Zhang , Lijia Xu","doi":"10.1016/j.rsci.2025.01.001","DOIUrl":"10.1016/j.rsci.2025.01.001","url":null,"abstract":"","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"32 2","pages":"Pages 131-136"},"PeriodicalIF":5.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Flooding in rice fields, especially in coastal regions and low-lying river basins, causes significant devastation to crops. Rice is highly susceptible to prolonged flooding, with a drastic decline in yields if inundation persists for more than 7 d, especially during the reproductive stage. Although the SUB1 QTL, which confers tolerance to complete submergence during the vegetative stage, has been incorporated into breeding programs, the development of alternative sources is crucial. These alternatives would broaden the genetic base, mitigate the influence of the genomic background, and extend the efficacy of SUB1 QTL to withstand longer submergence periods (up to approximately 21 d). Contemporary breeding strategies predominantly target submergence stress at the vegetative stage. However, stagnant flooding (partial submergence of vegetative parts) during the reproductive phase inflicts severe damage on the rice crop, leading to reduced yields, heightened susceptibility to pests and diseases, lodging, and inferior grain quality. The ability to tolerate stagnant flooding can be ascribed to several adaptive traits: accelerated aerenchyma formation, efficient underwater photosynthesis, reduced radial oxygen loss in submerged tissues, reinforced culms, enhanced reactive oxygen species scavenging within cells, dehydration tolerance post-flooding, and resistance to pests and diseases. A thorough investigation of the genetics underlying these traits, coupled with the integration of key alleles into elite genetic backgrounds, can significantly enhance food and income security in flood-prone rice-growing regions, particularly in coastal high-rainfall areas and low-lying river basins. This review aims to delineate an innovative breeding strategy that employs genomic, phenomic, and traditional breeding methodologies to develop rice varieties resilient to various dimensions of flooding stress at both the vegetative and reproductive stages.
{"title":"Discerning Genes to Deliver Varieties: Enhancing Vegetative- and Reproductive-Stage Flooding Tolerance in Rice","authors":"Sanchika Snehi , Kt Ravi Kiran , Sanket Rathi , Sameer Upadhyay , Suneetha Kota , Satish Kumar Sanwal , Bm Lokeshkumar , Arun Balasubramaniam , Nitish Ranjan Prakash , Pawan Kumar Singh","doi":"10.1016/j.rsci.2025.01.002","DOIUrl":"10.1016/j.rsci.2025.01.002","url":null,"abstract":"<div><div>Flooding in rice fields, especially in coastal regions and low-lying river basins, causes significant devastation to crops. Rice is highly susceptible to prolonged flooding, with a drastic decline in yields if inundation persists for more than 7 d, especially during the reproductive stage. Although the <em>SUB1</em> QTL, which confers tolerance to complete submergence during the vegetative stage, has been incorporated into breeding programs, the development of alternative sources is crucial. These alternatives would broaden the genetic base, mitigate the influence of the genomic background, and extend the efficacy of <em>SUB1</em> QTL to withstand longer submergence periods (up to approximately 21 d). Contemporary breeding strategies predominantly target submergence stress at the vegetative stage. However, stagnant flooding (partial submergence of vegetative parts) during the reproductive phase inflicts severe damage on the rice crop, leading to reduced yields, heightened susceptibility to pests and diseases, lodging, and inferior grain quality. The ability to tolerate stagnant flooding can be ascribed to several adaptive traits: accelerated aerenchyma formation, efficient underwater photosynthesis, reduced radial oxygen loss in submerged tissues, reinforced culms, enhanced reactive oxygen species scavenging within cells, dehydration tolerance post-flooding, and resistance to pests and diseases. A thorough investigation of the genetics underlying these traits, coupled with the integration of key alleles into elite genetic backgrounds, can significantly enhance food and income security in flood-prone rice-growing regions, particularly in coastal high-rainfall areas and low-lying river basins. This review aims to delineate an innovative breeding strategy that employs genomic, phenomic, and traditional breeding methodologies to develop rice varieties resilient to various dimensions of flooding stress at both the vegetative and reproductive stages.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"32 2","pages":"Pages 160-176"},"PeriodicalIF":5.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-01DOI: 10.1016/j.rsci.2024.11.001
Nie Lixiao , Guo Xiayu , Wang Weiqin , Qi Yucheng , Ai Zhiyong , He Aibin
Ratoon rice (Oryza sativa L.) is a sustainable planting model, and its planting area has been increasing year by year. However, there is a lack of literature reviewing the measures and mechanisms to regulate the regeneration rate, as well as the challenges in the production of ratoon rice. This study explores the effects of different varieties, climatic conditions (light and temperature), and cultivation measures (fertilizer management, cropping system, harvest method, water management, and plant growth regulators) on the regeneration rate and grain yield of the ratoon season. It summarizes and analyzes the possible mechanisms that affect the germination of regenerated buds from the perspectives of material accumulation and transportation, hormone metabolism, and molecular mechanisms, and identifies main factors currently limiting the development of ratoon rice. A significant positive correlation between the regeneration rate and grain yield of the ratoon season was found, regulated by varieties, temperatures, light resources, and cultivation measures. Improving the regeneration rate can effectively increase the production of ratoon rice. Notably, rice varieties with high regeneration ability exhibit characteristics such as a suitable growth period, a developed root system, high single-stem weight, a relatively small ratio of grain number to green leaf area, and strong lodging resistance in the main season. Additionally, the germination of regenerated buds is regulated by the accumulation and transport of endogenous hormones (indole-3-acetic acid, gibberellins, and cytokinins), photoassimilates (non-structural carbohydrates), and reactive oxygen metabolism. To further demonstrate the grain yield potential of the ratoon season, improvements are needed in three key areas: the cultivation system of low-stubble ratoon rice, the development of specialized harvesters, and the breeding of rice varieties with high-temperature tolerance during the main crop and low-temperature tolerance during the ratoon crop.
{"title":"Regulation of Regeneration Rate to Enhance Ratoon Rice Production","authors":"Nie Lixiao , Guo Xiayu , Wang Weiqin , Qi Yucheng , Ai Zhiyong , He Aibin","doi":"10.1016/j.rsci.2024.11.001","DOIUrl":"10.1016/j.rsci.2024.11.001","url":null,"abstract":"<div><div>Ratoon rice (<em>Oryza sativa</em> L.) is a sustainable planting model, and its planting area has been increasing year by year. However, there is a lack of literature reviewing the measures and mechanisms to regulate the regeneration rate, as well as the challenges in the production of ratoon rice. This study explores the effects of different varieties, climatic conditions (light and temperature), and cultivation measures (fertilizer management, cropping system, harvest method, water management, and plant growth regulators) on the regeneration rate and grain yield of the ratoon season. It summarizes and analyzes the possible mechanisms that affect the germination of regenerated buds from the perspectives of material accumulation and transportation, hormone metabolism, and molecular mechanisms, and identifies main factors currently limiting the development of ratoon rice. A significant positive correlation between the regeneration rate and grain yield of the ratoon season was found, regulated by varieties, temperatures, light resources, and cultivation measures. Improving the regeneration rate can effectively increase the production of ratoon rice. Notably, rice varieties with high regeneration ability exhibit characteristics such as a suitable growth period, a developed root system, high single-stem weight, a relatively small ratio of grain number to green leaf area, and strong lodging resistance in the main season. Additionally, the germination of regenerated buds is regulated by the accumulation and transport of endogenous hormones (indole-3-acetic acid, gibberellins, and cytokinins), photoassimilates (non-structural carbohydrates), and reactive oxygen metabolism. To further demonstrate the grain yield potential of the ratoon season, improvements are needed in three key areas: the cultivation system of low-stubble ratoon rice, the development of specialized harvesters, and the breeding of rice varieties with high-temperature tolerance during the main crop and low-temperature tolerance during the ratoon crop.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"32 2","pages":"Pages 177-192"},"PeriodicalIF":5.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-01DOI: 10.1016/j.rsci.2025.02.001
Ya Chen , Zhiquan Liu , Linyin Yang , Wu Fujie , Zijian Cao , Huanbin Shi , Jiehua Qiu , Yanjun Kou
The cell surface receptor chitin elicitor receptor kinase 1 (CERK1) is a well-known component of plant immunity. OsCERK1 is involved in regulating copper (Cu) uptake in rice, though the underlying mechanisms remain elusive. In this study, we identified proteins interacting with OsCERK1 and uncovered a novel heavy metal-associated domain-containing protein, OsHPP08. Our findings demonstrate that OsCERK1 phosphorylated and stabilized OsHPP08. Through structural analysis using AlphaFold, a yeast sensitivity assay of the Cu uptake-deficient yeast mutant, and Cu level measurements in oshpp08 mutants and overexpression plants (OsHPP08OE), we revealed that OsHPP08 facilitated Cu uptake. Additionally, rice seedling infection assays demonstrated that OsHPP08 positively contributed to blast resistance, with both OsCERK1 and OsHPP08 being essential for Cu-modulated blast resistance. Further analyses suggested that OsCERK1 and OsHPP08 likely enhanced blast resistance by regulating the antioxidant system and increasing H2O2 accumulation. In conclusion, OsCERK1 promoted Cu uptake by stabilizing OsHPP08, and together they contributed to Cu-modulated blast resistance, likely through the modulation of reactive oxygen species accumulation. These findings deepen our understanding of the intricate interplay between biotic and abiotic signals in rice.
{"title":"OsCERK1 Interacts with OsHPP08 to Regulate Copper Uptake and Blast Resistance in Rice","authors":"Ya Chen , Zhiquan Liu , Linyin Yang , Wu Fujie , Zijian Cao , Huanbin Shi , Jiehua Qiu , Yanjun Kou","doi":"10.1016/j.rsci.2025.02.001","DOIUrl":"10.1016/j.rsci.2025.02.001","url":null,"abstract":"<div><div>The cell surface receptor chitin elicitor receptor kinase 1 (CERK1) is a well-known component of plant immunity. OsCERK1 is involved in regulating copper (Cu) uptake in rice, though the underlying mechanisms remain elusive. In this study, we identified proteins interacting with OsCERK1 and uncovered a novel heavy metal-associated domain-containing protein, OsHPP08. Our findings demonstrate that OsCERK1 phosphorylated and stabilized OsHPP08. Through structural analysis using AlphaFold, a yeast sensitivity assay of the Cu uptake-deficient yeast mutant, and Cu level measurements in <em>oshpp08</em> mutants and overexpression plants (<em>OsHPP08OE</em>), we revealed that OsHPP08 facilitated Cu uptake. Additionally, rice seedling infection assays demonstrated that OsHPP08 positively contributed to blast resistance, with both OsCERK1 and OsHPP08 being essential for Cu-modulated blast resistance. Further analyses suggested that OsCERK1 and OsHPP08 likely enhanced blast resistance by regulating the antioxidant system and increasing H<sub>2</sub>O<sub>2</sub> accumulation. In conclusion, OsCERK1 promoted Cu uptake by stabilizing OsHPP08, and together they contributed to Cu-modulated blast resistance, likely through the modulation of reactive oxygen species accumulation. These findings deepen our understanding of the intricate interplay between biotic and abiotic signals in rice.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"32 2","pages":"Pages 203-216"},"PeriodicalIF":5.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.rsci.2024.08.008
Jeberlin Prabina Bright , Hemant S. Maheshwari , Sugitha Thangappan , Kahkashan Perveen , Najat A. Bukhari , Debasis Mitra , Riyaz Sayyed , Andrea Mastinu
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.
{"title":"Biofilmed-PGPR: Next-Generation Bioinoculant for Plant Growth Promotion in Rice under Changing Climate","authors":"Jeberlin Prabina Bright , Hemant S. Maheshwari , Sugitha Thangappan , Kahkashan Perveen , Najat A. Bukhari , Debasis Mitra , Riyaz Sayyed , Andrea Mastinu","doi":"10.1016/j.rsci.2024.08.008","DOIUrl":"10.1016/j.rsci.2024.08.008","url":null,"abstract":"<div><div>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 <em>Anabaena</em> AMP2, P-solubilizing <em>Bacillus megaterium</em> var<em>. phosphaticum</em> PB1, and K-solubilizing <em>Rhizobium pusense</em> 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 <em>in vitro</em> 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/hm<sup>2</sup> 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 (<em>r</em> = 0.92**) and soil chlorophyll content (<em>r</em> = 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.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"32 1","pages":"Pages 94-106"},"PeriodicalIF":5.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143378830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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