Current Plant Biology最新文献_第9页

Gene editing tools promote the development of chloroplast gene engineering 基因编辑工具促进了叶绿体基因工程的发展

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-30 DOI: 10.1016/j.cpb.2025.100540

Peng Xu , Chenxin Zhao , Shuxuan Li , Shuoxuan Li , Aifang Li , Jie Zhao , Aoqi Ma , Qianqian Wang , Dandan Guo , Jin Zhou , Shuying Feng

Plant genetic engineering serves as a crucial technology in enhancing crop quality, promoting pharmaceutical product biosynthesis, and changing agricultural practices. While conventional nuclear transgenic systems demonstrate generally stable and efficient transgene expression profiles, infrequent but persistent technical challenges-including gene silencing as well as low or unstable expression-continue to hinder precise genetic manipulation of nuclear genomes. Since the characteristics of maternal inheritance of plastid genome, chloroplast transformation circumvents this limitation and the risk of transgenic ecological pollution is greatly reduced. Although chloroplast gene engineering (CGE) has some unique advantages, it also has its own disadvantages, including low-efficiency transformation, a limited ability to target organelles, and a low number of species that can transform chloroplast genomes. Over the past few years, the establishment of several novel gene editing technologies has offered beneficial tools to solve these issues. This review explores advanced CGE tools (transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeats/CRISPR-associated systems, base editors, and prime editors) for sustainable agriculture, focusing on crop yield improvement, accelerated breeding of resistant varieties, enhanced stress tolerance, and optimized growth traits. Additionally, we thoroughly discuss the current challenges in CGE as well as its potential and future development. Moreover, new technologies and tools, such as nanotechnology, designer pentatricopeptide repeat proteins, and aptamers, are also considered with the aim of improving gene targeting and expression levels in CGE, which could potentially promote advances in CGE and extend its utility for different applications. Challenges in implementation and regulatory considerations are also discussed.

植物基因工程是提高作物质量、促进药品生物合成和改变农业生产方式的关键技术。虽然传统的核转基因系统显示出稳定和高效的转基因表达谱，但罕见但持续的技术挑战-包括基因沉默以及低或不稳定的表达-继续阻碍核基因组的精确遗传操作。由于质体基因组母系遗传的特点，叶绿体转化绕过了这一限制，大大降低了转基因生态污染的风险。尽管叶绿体基因工程（chloroplast gene engineering， CGE）具有一些独特的优势，但它也有自己的缺点，包括转化效率低、靶向细胞器的能力有限、能够转化叶绿体基因组的物种数量少。在过去的几年里，一些新的基因编辑技术的建立为解决这些问题提供了有益的工具。本文综述了用于可持续农业的先进的CGE工具（转录激活因子样效应核酸酶，聚集规律间隔短回文重复序列/ crispr相关系统，碱基编辑器和引物编辑器），重点是提高作物产量，加速抗性品种的选育，增强抗逆性和优化生长性状。此外，我们还深入讨论了通用电气目前面临的挑战，以及它的潜力和未来的发展。此外，新的技术和工具，如纳米技术、设计五肽重复蛋白和适体，也被认为是提高CGE基因靶向和表达水平的目的，这可能会促进CGE的进步，并扩大其在不同领域的应用。还讨论了实施和监管方面的挑战。

{"title":"Gene editing tools promote the development of chloroplast gene engineering","authors":"Peng Xu , Chenxin Zhao , Shuxuan Li , Shuoxuan Li , Aifang Li , Jie Zhao , Aoqi Ma , Qianqian Wang , Dandan Guo , Jin Zhou , Shuying Feng","doi":"10.1016/j.cpb.2025.100540","DOIUrl":"10.1016/j.cpb.2025.100540","url":null,"abstract":"<div><div>Plant genetic engineering serves as a crucial technology in enhancing crop quality, promoting pharmaceutical product biosynthesis, and changing agricultural practices. While conventional nuclear transgenic systems demonstrate generally stable and efficient transgene expression profiles, infrequent but persistent technical challenges-including gene silencing as well as low or unstable expression-continue to hinder precise genetic manipulation of nuclear genomes. Since the characteristics of maternal inheritance of plastid genome, chloroplast transformation circumvents this limitation and the risk of transgenic ecological pollution is greatly reduced. Although chloroplast gene engineering (CGE) has some unique advantages, it also has its own disadvantages, including low-efficiency transformation, a limited ability to target organelles, and a low number of species that can transform chloroplast genomes. Over the past few years, the establishment of several novel gene editing technologies has offered beneficial tools to solve these issues. This review explores advanced CGE tools (transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeats/CRISPR-associated systems, base editors, and prime editors) for sustainable agriculture, focusing on crop yield improvement, accelerated breeding of resistant varieties, enhanced stress tolerance, and optimized growth traits. Additionally, we thoroughly discuss the current challenges in CGE as well as its potential and future development. Moreover, new technologies and tools, such as nanotechnology, designer pentatricopeptide repeat proteins, and aptamers, are also considered with the aim of improving gene targeting and expression levels in CGE, which could potentially promote advances in CGE and extend its utility for different applications. Challenges in implementation and regulatory considerations are also discussed.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"44 ","pages":"Article 100540"},"PeriodicalIF":4.5,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144922432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessing the antiviral potential of Bacillus subtilis and Pseudomonas putida strains against tomato yellow leaf curl virus: A focus on BU018 and ZA102 枯草芽孢杆菌和恶臭假单胞菌菌株对番茄黄卷叶病毒的抗病毒潜力评价——以BU018和ZA102为例

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-30 DOI: 10.1016/j.cpb.2025.100541

Farshad Hemmati, Fatemeh Norouzi, Keramatollah Izadpanah, Alireza Afsharifar

Plant viruses are responsible for approximately half of all epidemic plant diseases and cause significant damage to agricultural products. The resistance of plants developed using traditional or genetic engineering methods can be overcome by the genomic flexibility of viruses. On the other hand, no effective antiviral compounds are currently available for on-farm use against viruses. Multiple pieces of evidence indicate the potential of various chemical compounds and beneficial microorganisms to induce resistance against viruses in plants. Therefore, introducing resistance-inducing compounds may be a significant strategy for viral disease management. In the present study, tomato yellow leaf curl virus (TYLCV), one of the most damaging tomato viruses worldwide, was used as a model, and the effect of several bacteria isolated from the rhizosphere on its control was investigated. The bacteria were collected from various tomato fields in different provinces of Iran and purified and identified. Several properties of these bacteria, including IAA, EPS, and HCN production, were also examined. Based on these characteristics and the local lesion test on Nicotiana glutinosa plants, two strains of bacteria were selected for the experiments. Tomato seedlings at the three-to four-leaf stage were inoculated with TYLCV and then treated individually and in combination with the two strains, Bacillus subtilis strain BU018 and Pseudomonas putida strain ZA102. The bioactive compounds present in these two strains were measured using GC-MS. Changes in plant defense enzymes (POD, SOD, and CAT), transcription levels of several pathogenesis-related genes (NPR1, PR1, and PDF1.2), disease severity, virus concentration, and plant growth indices were investigated. The two strains resulted in 36.84 % and 21.05 % reductions in disease severity, respectively, compared to the control. These findings were confirmed by other analyses, including changes in the activity of plant defense enzymes, transcription levels of pathogenesis-related genes, virus concentration, and plant growth indices, indicating a reduction in disease severity by these two strains.

植物病毒约占所有植物流行病的一半，并对农产品造成重大损害。利用传统或基因工程方法开发的植物的抗性可以通过病毒基因组的灵活性来克服。另一方面，目前还没有有效的抗病毒化合物可用于农场对抗病毒。多项证据表明，各种化合物和有益微生物具有诱导植物对病毒产生抗性的潜力。因此，引入耐药诱导化合物可能是病毒性疾病管理的重要策略。本研究以世界上危害最大的番茄病毒之一番茄黄卷叶病毒（TYLCV）为模型，研究了从番茄根际分离的几种细菌对其的防治效果。这些细菌是从伊朗不同省份的番茄田收集的，并进行了纯化和鉴定。这些细菌的一些特性，包括IAA， EPS和HCN的生产，也进行了检查。在此基础上，通过对烟叶植物的局部损伤试验，选择了两株病原菌进行试验。用TYLCV接种3 ~ 4叶期番茄幼苗，分别与枯草芽孢杆菌BU018和恶臭假单胞菌ZA102联合处理。采用气相色谱-质谱法测定了两株菌株的活性成分。研究了植物防御酶（POD、SOD和CAT）、几种致病相关基因（NPR1、PR1和PDF1.2）的转录水平、疾病严重程度、病毒浓度和植物生长指标的变化。与对照相比，这两种菌株的疾病严重程度分别降低了36.84 %和21.05 %。这些发现得到了其他分析的证实，包括植物防御酶活性、致病相关基因转录水平、病毒浓度和植物生长指数的变化，表明这两种菌株降低了疾病严重程度。

{"title":"Assessing the antiviral potential of Bacillus subtilis and Pseudomonas putida strains against tomato yellow leaf curl virus: A focus on BU018 and ZA102","authors":"Farshad Hemmati, Fatemeh Norouzi, Keramatollah Izadpanah, Alireza Afsharifar","doi":"10.1016/j.cpb.2025.100541","DOIUrl":"10.1016/j.cpb.2025.100541","url":null,"abstract":"<div><div>Plant viruses are responsible for approximately half of all epidemic plant diseases and cause significant damage to agricultural products. The resistance of plants developed using traditional or genetic engineering methods can be overcome by the genomic flexibility of viruses. On the other hand, no effective antiviral compounds are currently available for on-farm use against viruses. Multiple pieces of evidence indicate the potential of various chemical compounds and beneficial microorganisms to induce resistance against viruses in plants. Therefore, introducing resistance-inducing compounds may be a significant strategy for viral disease management. In the present study, tomato yellow leaf curl virus (TYLCV), one of the most damaging tomato viruses worldwide, was used as a model, and the effect of several bacteria isolated from the rhizosphere on its control was investigated. The bacteria were collected from various tomato fields in different provinces of Iran and purified and identified. Several properties of these bacteria, including IAA, EPS, and HCN production, were also examined. Based on these characteristics and the local lesion test on <em>Nicotiana glutinosa</em> plants, two strains of bacteria were selected for the experiments. Tomato seedlings at the three-to four-leaf stage were inoculated with TYLCV and then treated individually and in combination with the two strains, <em>Bacillus subtilis</em> strain BU018 and <em>Pseudomonas putida</em> strain ZA102. The bioactive compounds present in these two strains were measured using GC-MS. Changes in plant defense enzymes (POD, SOD, and CAT), transcription levels of several pathogenesis-related genes (NPR1, PR1, and PDF1.2), disease severity, virus concentration, and plant growth indices were investigated. The two strains resulted in 36.84 % and 21.05 % reductions in disease severity, respectively, compared to the control. These findings were confirmed by other analyses, including changes in the activity of plant defense enzymes, transcription levels of pathogenesis-related genes, virus concentration, and plant growth indices, indicating a reduction in disease severity by these two strains.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"44 ","pages":"Article 100541"},"PeriodicalIF":4.5,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144926786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Approaches and challenges in machine learning for monitoring agricultural products and predicting plant physiological responses to biotic and abiotic stresses 机器学习用于监测农产品和预测植物对生物和非生物胁迫的生理反应的方法和挑战

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-14 DOI: 10.1016/j.cpb.2025.100535

Saeedeh Zarbakhsh , Fazilat Fakhrzad , Dragana Rajkovic , Gniewko Niedbała , Magdalena Piekutowska

The world's population and the subsequent demand for food are increasing at an unprecedented rate, presenting significant challenges to sustainable food production. The impact of abiotic and biotic stresses on agricultural productivity is one of the major obstacles threatening food security. As a potential solution to these challenges, advancements in machine learning (ML) and deep learning (DL) based systems analyzing have emerged as promising solutions for improving crop yields, as well as mitigating plant stresses with high accuracy and efficiency. Furthermore, the increasing availability of sensor technologies and communication networks in the agriculture sector has led to the widespread adoption of ML for yield prediction and plant phenotyping, particularly on a large scale. The application of ML in conjunction with high-throughput imaging and genomic data is examined for early detection of physiological stress indicators and acceleration of crop improvement programs. This review highlights the latest technologies and approaches that are currently employed in ML and DL to effectively detect biotic and abiotic plant stresses. Despite notable progress, limitations persist in areas such as data quality, model generalization across agro-ecological zones, and field-level deployment. Emerging directions—including automated ML (AutoML), quantum machine learning, and digital twin technologies—are discussed as promising solutions for advancing precision agriculture and enhancing crop resilience under changing climatic conditions. These cutting-edge technologies have the potential to significantly enhance the sustainable production of food by efficient crop management and address the challenges posed by the growing global population and climate change, while mitigating the impacts of environmental and biotic stressors on crop production.

世界人口和随之而来的粮食需求正以前所未有的速度增长，对可持续粮食生产提出了重大挑战。非生物和生物胁迫对农业生产力的影响是威胁粮食安全的主要障碍之一。作为应对这些挑战的潜在解决方案，基于机器学习（ML）和深度学习（DL）的系统分析的进步已经成为提高作物产量以及高精度和高效率减轻植物胁迫的有希望的解决方案。此外，传感器技术和通信网络在农业领域的日益普及，导致ML在产量预测和植物表型分析中的广泛应用，特别是在大规模应用中。将机器学习与高通量成像和基因组数据相结合，用于生理胁迫指标的早期检测和作物改良计划的加速。本文综述了目前在ML和DL中用于有效检测生物和非生物植物胁迫的最新技术和方法。尽管取得了显著进展，但在数据质量、跨农业生态区模型推广和实地部署等领域仍然存在局限性。新兴方向——包括自动化机器学习（AutoML）、量子机器学习和数字孪生技术——作为推进精准农业和提高作物在不断变化的气候条件下的适应能力的有希望的解决方案进行了讨论。这些尖端技术有可能通过有效的作物管理显著提高粮食的可持续生产，应对全球人口增长和气候变化带来的挑战，同时减轻环境和生物压力源对作物生产的影响。

{"title":"Approaches and challenges in machine learning for monitoring agricultural products and predicting plant physiological responses to biotic and abiotic stresses","authors":"Saeedeh Zarbakhsh , Fazilat Fakhrzad , Dragana Rajkovic , Gniewko Niedbała , Magdalena Piekutowska","doi":"10.1016/j.cpb.2025.100535","DOIUrl":"10.1016/j.cpb.2025.100535","url":null,"abstract":"<div><div>The world's population and the subsequent demand for food are increasing at an unprecedented rate, presenting significant challenges to sustainable food production. The impact of abiotic and biotic stresses on agricultural productivity is one of the major obstacles threatening food security. As a potential solution to these challenges, advancements in machine learning (ML) and deep learning (DL) based systems analyzing have emerged as promising solutions for improving crop yields, as well as mitigating plant stresses with high accuracy and efficiency. Furthermore, the increasing availability of sensor technologies and communication networks in the agriculture sector has led to the widespread adoption of ML for yield prediction and plant phenotyping, particularly on a large scale. The application of ML in conjunction with high-throughput imaging and genomic data is examined for early detection of physiological stress indicators and acceleration of crop improvement programs. This review highlights the latest technologies and approaches that are currently employed in ML and DL to effectively detect biotic and abiotic plant stresses. Despite notable progress, limitations persist in areas such as data quality, model generalization across agro-ecological zones, and field-level deployment. Emerging directions—including automated ML (AutoML), quantum machine learning, and digital twin technologies—are discussed as promising solutions for advancing precision agriculture and enhancing crop resilience under changing climatic conditions. These cutting-edge technologies have the potential to significantly enhance the sustainable production of food by efficient crop management and address the challenges posed by the growing global population and climate change, while mitigating the impacts of environmental and biotic stressors on crop production.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100535"},"PeriodicalIF":4.5,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144864736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing drought tolerance in Cannabis sativa L. by Trichoderma hamatum through optimized water usage 通过优化水分利用，红木霉提高大麻耐旱性

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-08 DOI: 10.1016/j.cpb.2025.100534

Byeong-Ryeol Ryu , Gyeong-Ju Gim , Ye-Rim Shin , Min-Jun Kim , Min-Ji Kang , Tae-Hyung Kwon , Sang-Hyuck Park , Jung-Dae Lim

Drought stress in hemp (Cannabis sativa L.) is exacerbated by climate change, posing significant abiotic challenges. Trichoderma hamatum, known for mitigating abiotic stresses, was evaluated for its effects on hemp under drought conditions. Hemp plants were subjected to four conditions: control, drought stress, T. hamatum treatment, and T. hamatum with drought stress. Our results show that T. hamatum increases the photosynthesis rate by 303 % and the chlorophyll a and b contents by 29 % and 39 %, respectively, in drought-stressed hemp. T. hamatum treatment on hemp plants enhances the accumulation of secondary metabolites, such as total phenolic content (TPC) and total flavonoid content (TFC), which are crucial for non-enzymatic antioxidant defense mechanisms. Furthermore, the levels of these metabolites showed the greatest increase when treated in combination with drought stress. TPC and TFC were proportional to radical scavenging activities. This indicates that, unlike the antioxidant enzymes that increased only in the drought group, T. hamatum mitigates drought-induced oxidative stress by enhancing the accumulation of secondary metabolites such as phenolic compounds. Transcriptome analysis reveals that T. hamatum restores the overexpression of genes involved in the biosynthesis of proline and branched-chain amino acids, which are increased under drought stress. In the T. hamatum treatment, among the GO categories where more than half exhibited significant differences in expression, 90 % of aquaporin-related genes were upregulated, suggesting that the upregulated aquaporin-related genes enhance water use efficiency under limited water conditions, thereby alleviating drought stress in hemp.

气候变化加剧了大麻（Cannabis sativa L.）的干旱胁迫，带来了重大的非生物挑战。以减轻非生物胁迫而闻名的红木霉在干旱条件下对大麻的影响进行了评估。对大麻植株进行对照、干旱胁迫、柽柳处理和干旱胁迫下的柽柳处理。结果表明，在干旱胁迫下，柽柽树的光合速率提高了303 %，叶绿素a和b含量分别提高了29 %和39 %。麻霉处理增加了大麻次生代谢产物的积累，如总酚含量（TPC）和总黄酮含量（TFC），这是非酶抗氧化防御机制的关键。此外，这些代谢物的水平在干旱胁迫联合处理时表现出最大的增加。TPC和TFC与自由基清除活性成正比。这表明，与仅在干旱组中增加的抗氧化酶不同，柽柳通过增加次生代谢物（如酚类化合物）的积累来减轻干旱诱导的氧化应激。转录组分析表明，旱霉恢复了脯氨酸和支链氨基酸生物合成相关基因的过度表达，这些基因在干旱胁迫下增加。在毒麻处理中，在半数以上表达差异显著的氧化石墨烯类别中，90% %的水通道蛋白相关基因表达上调，这表明水通道蛋白相关基因的上调提高了大麻在有限水分条件下的水分利用效率，从而缓解了干旱胁迫。

{"title":"Enhancing drought tolerance in Cannabis sativa L. by Trichoderma hamatum through optimized water usage","authors":"Byeong-Ryeol Ryu , Gyeong-Ju Gim , Ye-Rim Shin , Min-Jun Kim , Min-Ji Kang , Tae-Hyung Kwon , Sang-Hyuck Park , Jung-Dae Lim","doi":"10.1016/j.cpb.2025.100534","DOIUrl":"10.1016/j.cpb.2025.100534","url":null,"abstract":"<div><div>Drought stress in hemp (<em>Cannabis sativa</em> L.) is exacerbated by climate change, posing significant abiotic challenges. <em>Trichoderma hamatum</em>, known for mitigating abiotic stresses, was evaluated for its effects on hemp under drought conditions. Hemp plants were subjected to four conditions: control, drought stress, <em>T. hamatum</em> treatment, and <em>T. hamatum</em> with drought stress. Our results show that <em>T. hamatum</em> increases the photosynthesis rate by 303 % and the chlorophyll a and b contents by 29 % and 39 %, respectively, in drought-stressed hemp. <em>T. hamatum</em> treatment on hemp plants enhances the accumulation of secondary metabolites, such as total phenolic content (TPC) and total flavonoid content (TFC), which are crucial for non-enzymatic antioxidant defense mechanisms. Furthermore, the levels of these metabolites showed the greatest increase when treated in combination with drought stress. TPC and TFC were proportional to radical scavenging activities. This indicates that, unlike the antioxidant enzymes that increased only in the drought group, <em>T. hamatum</em> mitigates drought-induced oxidative stress by enhancing the accumulation of secondary metabolites such as phenolic compounds. Transcriptome analysis reveals that <em>T. hamatum</em> restores the overexpression of genes involved in the biosynthesis of proline and branched-chain amino acids, which are increased under drought stress. In the <em>T. hamatum</em> treatment, among the GO categories where more than half exhibited significant differences in expression, 90 % of aquaporin-related genes were upregulated, suggesting that the upregulated aquaporin-related genes enhance water use efficiency under limited water conditions, thereby alleviating drought stress in hemp.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100534"},"PeriodicalIF":4.5,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144840759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The carotenoid biosynthesis pathway revealed to respond to Na2SiO3 stress on cotton growth 类胡萝卜素生物合成途径响应Na2SiO3胁迫对棉花生长的影响

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-07 DOI: 10.1016/j.cpb.2025.100532

Ruize Song , Xiao Chen , Yunxin He , Xuke Lu , Hao Lan , Yapeng Fan , Hui Huang , Yuping Sun , Menghao Zhang , Lidong Wang , Fange Wu , Xinrui Zhang , Xin Yu , Jie Jiang , Shuai Wang , Xiugui Chen , Junjuan Wang , Lixue Guo , Lanjie Zhao , Ling Li , Wuwei Ye

Silicon plays a dual role in plant growth. However, excessive application of sodium silicate (Na₂SiO₃), a commonly utilised Si-based fertiliser, can adversely affect plant development. In the present study, a pretreatment concentration of 20 mM Na₂SiO₃ was used to investigate its effect on the growth and development of cotton during the germination and three-leaf stages. The radicle necrosis rates of 84 upland cotton genotypes were assessed. RNA-seq analysis revealed 9098 differentially expressed genes (DEGs). Gene Ontology (GO) analysis revealed the enrichment of DEGs associated with various stimuli and stress responses. Concurrently, Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis identified the regulation of DEGs linked to the plant MAPK signalling pathway, lipid metabolism-related pathways, carotenoid biosynthesis pathway, plant hormone signal transduction, and secondary metabolite biosynthesis under Na₂SiO₃ stress. Notably, key genes within the carotenoid biosynthesis pathway were upregulated, suggesting that this pathway plays a significant role in mitigating oxidative damage. This study demonstrates that under saline-alkali stress conditions, excessive exogenous application of Na₂SiO₃ exacerbates toxicity in cotton plants. These findings provide a theoretical foundation for understanding the mechanisms underlying the response of cotton to Na₂SiO₃ stress and inform the judicious use of Si fertilisers.

硅在植物生长中起着双重作用。然而，过量施用硅酸钠（Na2SiO3）（一种常用的硅基肥料）会对植物发育产生不利影响。本研究以20 mM Na2SiO3为预处理浓度，研究其对棉花萌发期和三叶期生长发育的影响。对84个陆地棉基因型的胚根坏死率进行了评价。RNA-seq分析显示9098个差异表达基因（DEGs）。基因本体论（GO）分析显示，与各种刺激和应激反应相关的DEGs富集。同时，京都基因与基因组百科（KEGG）通路分析发现，在Na2SiO3胁迫下，与植物MAPK信号通路、脂质代谢相关通路、类胡萝卜素生物合成通路、植物激素信号转导和次生代谢物生物合成相关的DEGs受到调控。值得注意的是，类胡萝卜素生物合成途径中的关键基因被上调，表明该途径在减轻氧化损伤中起重要作用。本研究表明，在盐碱胁迫条件下，过量外源施用Na2SiO3会加剧棉花的毒性。这些发现为理解棉花对Na2SiO3胁迫的响应机制提供了理论基础，并为合理使用硅肥提供了依据。

{"title":"The carotenoid biosynthesis pathway revealed to respond to Na2SiO3 stress on cotton growth","authors":"Ruize Song , Xiao Chen , Yunxin He , Xuke Lu , Hao Lan , Yapeng Fan , Hui Huang , Yuping Sun , Menghao Zhang , Lidong Wang , Fange Wu , Xinrui Zhang , Xin Yu , Jie Jiang , Shuai Wang , Xiugui Chen , Junjuan Wang , Lixue Guo , Lanjie Zhao , Ling Li , Wuwei Ye","doi":"10.1016/j.cpb.2025.100532","DOIUrl":"10.1016/j.cpb.2025.100532","url":null,"abstract":"<div><div>Silicon plays a dual role in plant growth. However, excessive application of sodium silicate (Na<sub>2</sub>SiO<sub>3</sub>), a commonly utilised Si-based fertiliser, can adversely affect plant development. In the present study, a pretreatment concentration of 20 mM Na<sub>2</sub>SiO<sub>3</sub> was used to investigate its effect on the growth and development of cotton during the germination and three-leaf stages. The radicle necrosis rates of 84 upland cotton genotypes were assessed. RNA-seq analysis revealed 9098 differentially expressed genes (DEGs). Gene Ontology (GO) analysis revealed the enrichment of DEGs associated with various stimuli and stress responses. Concurrently, Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis identified the regulation of DEGs linked to the plant MAPK signalling pathway, lipid metabolism-related pathways, carotenoid biosynthesis pathway, plant hormone signal transduction, and secondary metabolite biosynthesis under Na<sub>2</sub>SiO<sub>3</sub> stress. Notably, key genes within the carotenoid biosynthesis pathway were upregulated, suggesting that this pathway plays a significant role in mitigating oxidative damage. This study demonstrates that under saline-alkali stress conditions, excessive exogenous application of Na<sub>2</sub>SiO<sub>3</sub> exacerbates toxicity in cotton plants. These findings provide a theoretical foundation for understanding the mechanisms underlying the response of cotton to Na<sub>2</sub>SiO<sub>3</sub> stress and inform the judicious use of Si fertilisers.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100532"},"PeriodicalIF":4.5,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144809481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolomic and transcriptomic analysis reveals high light to promote tuber enlargement through starch accumulation in Pinellia ternata 代谢组学和转录组学分析表明，强光通过淀粉积累促进半夏块茎膨大

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-05 DOI: 10.1016/j.cpb.2025.100529

Duan Wu, Qin Chang, Minting Lu, Qi shen

Pinellia ternata (Thunb.) Breit, a vital traditional Chinese medicinal plant, responds distinctively to high light conditions. To reveal that light signal regulate material transport and accumulation in P. ternata, integrated analyses of metabolomic, hormone levels, full - length transcriptome sequencing, and RNA-seq were carried out. High light inhibits growth and chlorophyll accumulation of P. ternata, but activates the photoprotective system and significantly promoting tuber enlargement and increasing starch accumulation by 24.92 % in tubers. In tubers of P. ternata, 210 DAMs and 1459 DEGs were enriched in key pathways like photosynthesis, hormone signaling transduction and starch and sucrose metabolism. High light promotes the expression of genes that are involved in the synthesis of stress - responsive hormones such as JA, ABA, IAA and SA, as well as the expression of stress response factors (mTERF, GNAT) in the leaves of P. ternata, but reduces the accumulation of these hormone in tubers. Simultaneously, high light inhibits the expression of light signal-responsive genes (e.g., PIF4, CCA1, and PHYA) and upregulates genes involved in phototropism (PHOT2) and chlorophyll biosynthesis (e.g., GluTR, GSAM, UROD, COPRO genⅢ-Ox). Additionally, by activating the expression of genes encoding sugar transporters (pGlcTs, PMT, TMTs, SWEETs) and genes related to starch and sucrose synthases (SS, SPS, SBE, GBSSI, AGPase), high light facilitates the conversion of monosaccharides, including fructose and glucose, into starch for accumulation, thereby promoting the swelling of tubers. The proposed mechanism indicates high-light activation of photoprotection and energy conversion promotes sugar and photosynthetic product handling, facilitating tuber growth. This research offers novel insights into light - regulation in P. ternata, guiding its high - yield cultivation and enhancing understanding of its adaptation to high-light environments.

半夏（Pinellia ternata）布雷特是一种重要的传统中药植物，对强光条件有独特的反应。为了揭示光信号对P. ternata物质转运和积累的调控作用，我们对其代谢组学、激素水平、全长转录组测序和RNA-seq进行了综合分析。强光抑制了紫菜的生长和叶绿素积累，但激活了光保护系统，显著促进了块茎膨大，增加了24.92 %的淀粉积累。在块茎中，210个dam和1459个deg在光合作用、激素信号转导、淀粉和蔗糖代谢等关键途径中富集。强光促进了叶片中JA、ABA、IAA、SA等胁迫应答激素合成相关基因的表达以及胁迫应答因子（mTERF、GNAT）的表达，但减少了这些激素在块茎中的积累。同时，强光抑制光信号响应基因（如PIF4、CCA1和PHYA）的表达，上调参与向光性（PHOT2）和叶绿素生物合成的基因（如GluTR、GSAM、UROD、COPRO genⅢ-Ox）。此外，通过激活编码糖转运蛋白的基因（pGlcTs， PMT, TMTs, SWEETs）和淀粉和蔗糖合成酶相关基因（SS， SPS， SBE， GBSSI, AGPase）的表达，强光促进了单糖（包括果糖和葡萄糖）转化为淀粉积累，从而促进块茎肿胀。该机制表明，高光激活的光保护和能量转换促进了糖和光合产物的处理，促进了块茎的生长。本研究为深入了解柽柳的光调控机制提供了新的思路，为柽柳高产栽培提供了指导，为柽柳对强光环境的适应提供了新的认识。

{"title":"Metabolomic and transcriptomic analysis reveals high light to promote tuber enlargement through starch accumulation in Pinellia ternata","authors":"Duan Wu, Qin Chang, Minting Lu, Qi shen","doi":"10.1016/j.cpb.2025.100529","DOIUrl":"10.1016/j.cpb.2025.100529","url":null,"abstract":"<div><div><em>Pinellia ternata</em> (Thunb.) Breit, a vital traditional Chinese medicinal plant, responds distinctively to high light conditions. To reveal that light signal regulate material transport and accumulation in <em>P. ternata</em>, integrated analyses of metabolomic, hormone levels, full - length transcriptome sequencing, and RNA-seq were carried out. High light inhibits growth and chlorophyll accumulation of <em>P. ternata</em>, but activates the photoprotective system and significantly promoting tuber enlargement and increasing starch accumulation by 24.92 % in tubers. In tubers of <em>P. ternata</em>, 210 DAMs and 1459 DEGs were enriched in key pathways like photosynthesis, hormone signaling transduction and starch and sucrose metabolism. High light promotes the expression of genes that are involved in the synthesis of stress - responsive hormones such as JA, ABA, IAA and SA, as well as the expression of stress response factors (<em>mTERF</em>, <em>GNAT</em>) in the leaves of <em>P. ternata</em>, but reduces the accumulation of these hormone in tubers. Simultaneously, high light inhibits the expression of light signal-responsive genes (e.g., <em>PIF4</em>, <em>CCA1</em>, and <em>PHYA</em>) and upregulates genes involved in phototropism (<em>PHOT2</em>) and chlorophyll biosynthesis (e.g., <em>GluTR</em>, <em>GSAM</em>, <em>UROD</em>, <em>COPRO genⅢ-Ox</em>). Additionally, by activating the expression of genes encoding sugar transporters (<em>pGlcTs</em>, <em>PMT</em>, <em>TMTs</em>, <em>SWEETs</em>) and genes related to starch and sucrose synthases (<em>SS</em>, <em>SPS</em>, <em>SBE</em>, <em>GBSSI</em>, <em>AGPase</em>), high light facilitates the conversion of monosaccharides, including fructose and glucose, into starch for accumulation, thereby promoting the swelling of tubers. The proposed mechanism indicates high-light activation of photoprotection and energy conversion promotes sugar and photosynthetic product handling, facilitating tuber growth. This research offers novel insights into light - regulation in <em>P. ternata</em>, guiding its high - yield cultivation and enhancing understanding of its adaptation to high-light environments.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"44 ","pages":"Article 100529"},"PeriodicalIF":4.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome wide association mapping reveals genetic loci and candidate genes for seedling stage drought tolerance in lentil (Lens culinaris) 小扁豆（Lens culinaris）苗期抗旱性遗传位点和候选基因的全基因组关联定位

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-05 DOI: 10.1016/j.cpb.2025.100531

Neteti Siddartha Kumar , Renu Pandey , Anjali Anand , Amit Kumar Singh , Muraleedhar S. Aski , Gyan Prakash Mishra , Harsh Kumar Dikshit , Mahesh Rao , R.S. Bana , Shiv Kumar , Viswanathan Chinnusamy , Ruchi Bansal

Lentil (Lens culinaris) is a very important cold-season nutritious legume crop. The crop faces intermittent drought in South Asian countries and terminal drought in West Asian and North African Mediterranean regions causing adverse impact on lentil productivity. The present study aimed to evaluate a diverse lentil panel (243 genotypes) under irrigated and drought conditions at seedling stage and to identify significant marker trait associations for drought tolerance traits. Drought stress was imposed by restricting the pre-sowing irrigation. A total of 18 different morpho-physiological traits including root (length, surface area, volume, tips and forks), physiological (germination percentage, NDVI, canopy temperature) and growth (seedling vigor, plant biomass) traits were recorded among the lentil genotypes in both control and stress conditions. All the traits except canopy temperature were found to be significantly reduced under stress. Principal component analysis explained 56.3 % variation in control and 60.7 % variation in drought condition. Shoot dry weight had significant correlation to NDVI, shoot branching, primary and total root length, and root length density. Genotypes IC560032, IC560246, P3227, IC560051, and IG134349 were identified as drought-tolerant using SSI (<0.5). Association mapping analysis identified 65 and 71 non-overlapping distinct SNPs significantly associated with all traits under control and drought conditions, respectively. Putative candidate genes encoding legumain-like cysteine endopeptidase, L-ascorbate oxidase, and auxin-responsive proteins were involved in the regulation of key drought tolerance associated traits like germination percentage, root length, seedling vigor respectively. These findings highlight the potential of lentil germplasm for drought resilience and provide a valuable genetic resource for breeding high-yielding, stress-tolerant varieties.

小扁豆（Lens culinaris）是一种非常重要的冷季营养豆科作物。该作物在南亚国家面临间歇性干旱，在西亚和北非地中海地区面临终末干旱，对扁豆生产力造成不利影响。本研究旨在评估一个不同的小扁豆群体（243个基因型）在苗期灌溉和干旱条件下的耐旱性，并确定显著的标记性状相关性。通过限制播前灌溉施加干旱胁迫。在对照和胁迫条件下，共记录了18个不同的形态生理性状，包括根（长度、表面积、体积、尖端和分叉）、生理（发芽率、NDVI、冠层温度）和生长（幼苗活力、植株生物量）。除冠层温度外，其余性状均显著降低。主成分分析解释了对照和干旱条件下56.3% %和60.7 %的变异。地上部干重与NDVI、地上部分枝、主根长和总根长、根长密度呈极显著相关。基因型IC560032、IC560246、P3227、IC560051和IG134349通过SSI （<0.5）鉴定为耐旱基因型。关联图谱分析发现，在对照和干旱条件下，65个和71个非重叠的不同snp与所有性状均显著相关。编码豆科类半胱氨酸内肽酶、l -抗坏血酸氧化酶和生长素响应蛋白的候选基因分别参与了发芽率、根长、幼苗活力等关键抗旱相关性状的调控。这些发现突出了扁豆种质的抗旱潜力，为培育高产耐旱品种提供了宝贵的遗传资源。

{"title":"Genome wide association mapping reveals genetic loci and candidate genes for seedling stage drought tolerance in lentil (Lens culinaris)","authors":"Neteti Siddartha Kumar , Renu Pandey , Anjali Anand , Amit Kumar Singh , Muraleedhar S. Aski , Gyan Prakash Mishra , Harsh Kumar Dikshit , Mahesh Rao , R.S. Bana , Shiv Kumar , Viswanathan Chinnusamy , Ruchi Bansal","doi":"10.1016/j.cpb.2025.100531","DOIUrl":"10.1016/j.cpb.2025.100531","url":null,"abstract":"<div><div>Lentil (<em>Lens culinaris</em>) is a very important cold-season nutritious legume crop. The crop faces intermittent drought in South Asian countries and terminal drought in West Asian and North African Mediterranean regions causing adverse impact on lentil productivity. The present study aimed to evaluate a diverse lentil panel (243 genotypes) under irrigated and drought conditions at seedling stage and to identify significant marker trait associations for drought tolerance traits. Drought stress was imposed by restricting the pre-sowing irrigation. A total of 18 different morpho-physiological traits including root (length, surface area, volume, tips and forks), physiological (germination percentage, NDVI, canopy temperature) and growth (seedling vigor, plant biomass) traits were recorded among the lentil genotypes in both control and stress conditions. All the traits except canopy temperature were found to be significantly reduced under stress. Principal component analysis explained 56.3 % variation in control and 60.7 % variation in drought condition. Shoot dry weight had significant correlation to NDVI, shoot branching, primary and total root length, and root length density. Genotypes IC560032, IC560246, P3227, IC560051, and IG134349 were identified as drought-tolerant using SSI (<0.5). Association mapping analysis identified 65 and 71 non-overlapping distinct SNPs significantly associated with all traits under control and drought conditions, respectively. Putative candidate genes encoding legumain-like cysteine endopeptidase, <span>L</span>-ascorbate oxidase, and auxin-responsive proteins were involved in the regulation of key drought tolerance associated traits like germination percentage, root length, seedling vigor respectively. These findings highlight the potential of lentil germplasm for drought resilience and provide a valuable genetic resource for breeding high-yielding, stress-tolerant varieties.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100531"},"PeriodicalIF":4.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144864735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phenotypic evaluation of worldwide germplasm of arugula (Eruca sativa Mill.) and identification of underlying latent factors contributing to phenotypic variation under indoor farming conditions 室内栽培条件下世界范围内芝麻菜种质的表型评价及引起表型变异的潜在因素鉴定

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-05 DOI: 10.1016/j.cpb.2025.100528

Seam Choon Law , Ting Xiang Neik , Ethan Tze Cherng Lim , Adrian Ming Jern Lee , Yi Lin Lim , Wan Zu Tang , Shuang Song , Pei-Wen Ong , Sin Joe Ng , Fook Tim Chew

Eruca sativa (arugula) is often consumed fresh in regions where raw salads are a dietary staple. Studies investigating the phenotypic diversity of E. sativa have been reported in the past differentiating them by gene pools according to geographical origins. We expanded the scope of analysis to include deep phenotypes, and the diversity of germplasm. Furthermore, there is no report of such crop being evaluated in a large scale under indoor farming conditions. In this study, 185 accessions were subjected to phenotypic evaluation across 68 phenotypic traits. High-throughput phenotyping machines and image processing platforms employed were efficient to measure vegetative yield-, hyperspectral-, and plant architecture-related traits of E. sativa. Wide phenotypic variations were evidenced in the collection and significant differences were observed between accessions in majority of the traits evaluated. The population genetic structure divided the germplasm collection into three major continental clusters (Asia, Africa, and Europe). In addition, the three major continental clusters also showed significant differences in the tendency to flower early, vegetative leafy plant yield, plant height, vegetative index, hairiness and leaf blade color. Factor analysis revealed nine underlying latent factors contributing approximately 70 % of the total phenotypic variations, with each potentially enhancing crop’s productivity and quality. Based on desirable agronomic traits that are suitable for controlled environment agriculture (CEA), bivariate analysis was conducted using four latent factors (Total yield-, plant height-, post-harvest-, and flowering-related). Subsequently, three ideal accessions (ERU12, PI 178901, and PI 251491) were highlighted as high-yielding, short, long shelf-life crops for potential future plant breeding and genetic improvement.

在以生沙拉为主食的地区，芝麻菜通常是新鲜食用的。在过去的研究中，已经报道了苜蓿的表型多样性，并根据地理来源通过基因库进行了区分。我们扩大了分析的范围，包括深层表型和种质多样性。此外，还没有在室内耕作条件下对这种作物进行大规模评价的报告。在本研究中，185份材料进行了68个表型性状的表型评价。采用高通量表型机和图像处理平台有效地测量了sativa的营养产量、高光谱和植物结构相关性状。广泛的表型差异在收集中被证明，并且在大多数被评估的性状中观察到显著差异。种群遗传结构将种质资源集合划分为三个主要的大陆群（亚洲、非洲和欧洲）。此外，3个主要大陆集群在早花倾向、营养叶产量、株高、营养指数、毛羽和叶片颜色等方面也存在显著差异。因子分析显示，9个潜在因子贡献了约70% %的总表型变异，每个因子都可能提高作物的生产力和质量。以适宜控制环境农业（CEA）的理想农艺性状为基础，利用4个潜在因子（总产量、株高、采收后和开花相关）进行双变量分析。结果表明，ERU12、PI 178901和PI 251491是高产、短、长保质期的理想作物，具有潜在的育种和遗传改良潜力。

{"title":"Phenotypic evaluation of worldwide germplasm of arugula (Eruca sativa Mill.) and identification of underlying latent factors contributing to phenotypic variation under indoor farming conditions","authors":"Seam Choon Law , Ting Xiang Neik , Ethan Tze Cherng Lim , Adrian Ming Jern Lee , Yi Lin Lim , Wan Zu Tang , Shuang Song , Pei-Wen Ong , Sin Joe Ng , Fook Tim Chew","doi":"10.1016/j.cpb.2025.100528","DOIUrl":"10.1016/j.cpb.2025.100528","url":null,"abstract":"<div><div><em>Eruca sativa</em> (arugula) is often consumed fresh in regions where raw salads are a dietary staple. Studies investigating the phenotypic diversity of <em>E. sativa</em> have been reported in the past differentiating them by gene pools according to geographical origins. We expanded the scope of analysis to include deep phenotypes, and the diversity of germplasm. Furthermore, there is no report of such crop being evaluated in a large scale under indoor farming conditions. In this study, 185 accessions were subjected to phenotypic evaluation across 68 phenotypic traits. High-throughput phenotyping machines and image processing platforms employed were efficient to measure vegetative yield-, hyperspectral-, and plant architecture-related traits of <em>E. sativa</em>. Wide phenotypic variations were evidenced in the collection and significant differences were observed between accessions in majority of the traits evaluated. The population genetic structure divided the germplasm collection into three major continental clusters (Asia, Africa, and Europe). In addition, the three major continental clusters also showed significant differences in the tendency to flower early, vegetative leafy plant yield, plant height, vegetative index, hairiness and leaf blade color. Factor analysis revealed nine underlying latent factors contributing approximately 70 % of the total phenotypic variations, with each potentially enhancing crop’s productivity and quality. Based on desirable agronomic traits that are suitable for controlled environment agriculture (CEA), bivariate analysis was conducted using four latent factors (Total yield-, plant height-, post-harvest-, and flowering-related). Subsequently, three ideal accessions (ERU12, PI 178901, and PI 251491) were highlighted as high-yielding, short, long shelf-life crops for potential future plant breeding and genetic improvement.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100528"},"PeriodicalIF":4.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144779648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Decoding stress specific transcriptional regulation by causality aware Graph-Transformer deep learning 通过因果关系感知Graph-Transformer深度学习解码压力特定转录调节

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-05 DOI: 10.1016/j.cpb.2025.100521

Umesh Bhati , Akanksha Sharma , Sagar Gupta , Anchit Kumar , Upendra Kumar Pradhan , Ravi Shankar

Cells respond to environmental stimuli through transcriptional reprogramming orchestrated by transcription factors (TFs) which interpret cis-regulatory DNA sequences to determine the timing and locations of gene expression. The diversification of TFs and their interactions with cis-regulatory elements (CREs) underpins plant adaptation to stress through the formation of gene regulatory networks (GRNs). However, deciphering condition-specific GRNs through selective TF bindings for spatio-temporal gene expression remains major challenge in plant biology. To decipher that the present study brings forward a novel computational framework designed to reason about the spatio-temporal dynamics of TF interaction. Leveraging over ∼23TB of multi-omics data (ChIP-seq, RNA-seq, and protein-protein interaction), a system of Bayesian causal networks was raised. It is capable of explaining TF’s conditional bindings across diverse conditions for Arabidopsis. These networks, validated against extensive experimental data, became input to a Graph Transformer deep learning system. Models were developed for 110 abiotic stress-related TFs, enabling accurate condition-specific detection of TF binding directly from RNA-seq data, bypassing the need for separate ChIP-seq experiments. The approach, CTF-BIND achieved a high average accuracy of ∼93 % when tested against a large volume of experimentally established data from various conditions. It is implemented as an interactive, open-access web server and database which captures dynamic shifts in regulatory pathways. CTF-BIND revolutionizes TF condition-specific binding identification with deep-learning, offering a cost-effective alternative to ChIP-seq. It is expected to accelerate the research towards crop improvement strategies. CTF-BIND is freely available as a web server at https://hichicob.ihbt.res.in/ctfbind/.

细胞通过转录因子（tf）的转录重编程来响应环境刺激，转录因子解释顺式调控DNA序列，以确定基因表达的时间和位置。TFs的多样化及其与顺式调控元件（CREs）的相互作用是植物通过形成基因调控网络（grn）来适应逆境的基础。然而，通过选择性TF结合时空基因表达来破译条件特异性grn仍然是植物生物学的主要挑战。为了解释这一点，本研究提出了一个新的计算框架，旨在解释TF相互作用的时空动态。利用超过23TB的多组学数据（ChIP-seq、RNA-seq和蛋白质-蛋白质相互作用），建立了一个贝叶斯因果网络系统。它能够解释TF在不同条件下对拟南芥的条件结合。这些网络经过大量实验数据的验证，成为Graph Transformer深度学习系统的输入。为110种非生物应激相关TF建立了模型，可以直接从RNA-seq数据中准确检测TF结合的条件特异性，而无需单独的ChIP-seq实验。该方法，CTF-BIND在针对来自各种条件的大量实验建立的数据进行测试时，达到了~ 93 %的高平均精度。它是作为一个交互式的、开放访问的web服务器和数据库来实现的，它可以捕捉监管途径中的动态变化。CTF-BIND通过深度学习彻底改变了TF条件特异性结合识别，为ChIP-seq提供了经济有效的替代方案。它有望加速作物改良策略的研究。CTF-BIND作为web服务器可在https://hichicob.ihbt.res.in/ctfbind/免费获得。

{"title":"Decoding stress specific transcriptional regulation by causality aware Graph-Transformer deep learning","authors":"Umesh Bhati , Akanksha Sharma , Sagar Gupta , Anchit Kumar , Upendra Kumar Pradhan , Ravi Shankar","doi":"10.1016/j.cpb.2025.100521","DOIUrl":"10.1016/j.cpb.2025.100521","url":null,"abstract":"<div><div>Cells respond to environmental stimuli through transcriptional reprogramming orchestrated by transcription factors (TFs) which interpret cis-regulatory DNA sequences to determine the timing and locations of gene expression. The diversification of TFs and their interactions with cis-regulatory elements (CREs) underpins plant adaptation to stress through the formation of gene regulatory networks (GRNs). However, deciphering condition-specific GRNs through selective TF bindings for spatio-temporal gene expression remains major challenge in plant biology. To decipher that the present study brings forward a novel computational framework designed to reason about the spatio-temporal dynamics of TF interaction. Leveraging over ∼23TB of multi-omics data (ChIP-seq, RNA-seq, and protein-protein interaction), a system of Bayesian causal networks was raised. It is capable of explaining TF’s conditional bindings across diverse conditions for <em>Arabidopsis</em>. These networks, validated against extensive experimental data, became input to a Graph Transformer deep learning system. Models were developed for 110 abiotic stress-related TFs, enabling accurate condition-specific detection of TF binding directly from RNA-seq data, bypassing the need for separate ChIP-seq experiments. The approach, CTF-BIND achieved a high average accuracy of ∼93 % when tested against a large volume of experimentally established data from various conditions. It is implemented as an interactive, open-access web server and database which captures dynamic shifts in regulatory pathways. CTF-BIND revolutionizes TF condition-specific binding identification with deep-learning, offering a cost-effective alternative to ChIP-seq. It is expected to accelerate the research towards crop improvement strategies. CTF-BIND is freely available as a web server at <span><span>https://hichicob.ihbt.res.in/ctfbind/</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100521"},"PeriodicalIF":4.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144829236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcription factors participate in methyl jasmonate-induced diterpenoid biosynthesis in Andrographis paniculata 转录因子参与茉莉酸甲酯诱导穿心莲二萜类生物合成

IF 4.5 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-08-05 DOI: 10.1016/j.cpb.2025.100530

Yuan Li , Yue Shi , Yong Fan , Guangxi Ren , Dan Jiang , Kuangwei Cao , Yaogong Zhang , Zhengyan Li , Da Li , Chunsheng Liu

Andrographis paniculata is renowned for its wide range of pharmaceutical properties, largely owing to the presence of bioactive diterpenoids. However, the mechanism of methyl jasmonate (MeJA) -induced diterpenoid biosynthesis in A. paniculata remains poorly understood. In this study, we found that the MeJA-induced accumulation of diterpenoids was attributed to the increased expression of genes involved in diterpenoid biosynthetic pathways. Transient overexpression and Y1H assays revealed that ApMYC2, ApbZIP46, and ApWRKY33 were positive regulators that promoted the accumulation of diterpenoids by directly binding to the promoters of the downstream target gene ApUGT76E1. Thus, ApMYC2, ApbZIP46, and ApWRKY33 may be involved in the regulation of the diterpenoid biosynthesis pathway in A. paniculata. Overall, this research lays the groundwork for elucidating the molecular mechanism by which MYCs, bZIPs and WRKYs regulate the accumulation of diterpenoids in A. paniculata under MeJA induction. Our results provide a theoretical basis for the molecular breeding and quality improvement of A. paniculata in the future.

穿心莲以其广泛的药用特性而闻名，这主要是由于其生物活性二萜的存在。然而，茉莉酸甲酯（MeJA）诱导的甲草二萜类生物合成机制尚不清楚。在这项研究中，我们发现meja诱导的二萜积累归因于参与二萜生物合成途径的基因表达增加。瞬时过表达和Y1H实验显示，ApMYC2、ApbZIP46和ApWRKY33是正向调节因子，通过直接结合下游靶基因ApUGT76E1的启动子促进二萜的积累。因此，ApMYC2、ApbZIP46和ApWRKY33可能参与了金针桃二萜类生物合成途径的调控。综上所述，本研究为阐明MYCs、bZIPs和WRKYs在MeJA诱导下调控金穗二萜类物质积累的分子机制奠定了基础。本研究结果为今后金银花的分子育种和品质改良提供了理论依据。

{"title":"Transcription factors participate in methyl jasmonate-induced diterpenoid biosynthesis in Andrographis paniculata","authors":"Yuan Li , Yue Shi , Yong Fan , Guangxi Ren , Dan Jiang , Kuangwei Cao , Yaogong Zhang , Zhengyan Li , Da Li , Chunsheng Liu","doi":"10.1016/j.cpb.2025.100530","DOIUrl":"10.1016/j.cpb.2025.100530","url":null,"abstract":"<div><div><em>Andrographis paniculata</em> is renowned for its wide range of pharmaceutical properties, largely owing to the presence of bioactive diterpenoids. However, the mechanism of methyl jasmonate (MeJA) -induced diterpenoid biosynthesis in <em>A. paniculata</em> remains poorly understood. In this study, we found that the MeJA-induced accumulation of diterpenoids was attributed to the increased expression of genes involved in diterpenoid biosynthetic pathways. Transient overexpression and Y1H assays revealed that <em>ApMYC2</em>, <em>ApbZIP46</em>, and <em>ApWRKY33</em> were positive regulators that promoted the accumulation of diterpenoids by directly binding to the promoters of the downstream target gene <em>ApUGT76E1</em>. Thus, <em>ApMYC2</em>, <em>ApbZIP46</em>, and <em>ApWRKY33</em> may be involved in the regulation of the diterpenoid biosynthesis pathway in <em>A. paniculata</em>. Overall, this research lays the groundwork for elucidating the molecular mechanism by which <em>MYC</em>s, <em>bZIP</em>s and <em>WRKY</em>s regulate the accumulation of diterpenoids in <em>A. paniculata</em> under MeJA induction. Our results provide a theoretical basis for the molecular breeding and quality improvement of <em>A. paniculata</em> in the future.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100530"},"PeriodicalIF":4.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144771087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0