Current Plant Biology最新文献

{"title":"Gene editing tools promote the development of chloroplast gene engineering","authors":"Peng Xu ,&nbsp;Chenxin Zhao ,&nbsp;Shuxuan Li ,&nbsp;Shuoxuan Li ,&nbsp;Aifang Li ,&nbsp;Jie Zhao ,&nbsp;Aoqi Ma ,&nbsp;Qianqian Wang ,&nbsp;Dandan Guo ,&nbsp;Jin Zhou ,&nbsp;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}

{"title":"The yeast Papiliotrema laurentii alleviates drought-induced stress in maize and affects oxidative status, LEA genes, hormone concentrations, and fatty acid allocation","authors":"Marko Bajus ,&nbsp;Zuzana Vivodová ,&nbsp;Michaela Bačovčinová ,&nbsp;Eva Labancová ,&nbsp;Danica Kučerová ,&nbsp;Ágnes Horváthová ,&nbsp;Kristína Holeková ,&nbsp;Diana Hačkuličová ,&nbsp;Renáta Vadkertiová ,&nbsp;Karin Kollárová","doi":"10.1016/j.cpb.2025.100542","DOIUrl":"10.1016/j.cpb.2025.100542","url":null,"abstract":"<div><div>Drought stress can significantly affect maize growth; hence, new substances with a potential to alleviate drought-induced damage in plants are being investigated. Here, we studied the biostimulant potential and mechanisms of the yeast <em>Papiliotrema laurentii</em> CCY 17–3–24. The maize grains were treated with <em>P. laurentii</em> suspensions of different yeast concentrations (10⁶, 10⁷, 10⁸, and 10⁹ cells ml⁻¹) during the imbibition and germination. The yeast did not have plant-growth promoting effects in well-watered plants; however, it stimulated the growth of the drought-stressed maize in the concentration 10⁷ cells ml⁻¹ (e.g., shoot dry weight by 21.6 %). Furthermore, the relative water content and oxidative stress were improved in plants treated with the yeast compared to drought-stressed plants (e.g., decreased H₂O₂ concentration by 46.1 % in roots). The expression of <em>LEA</em> genes, which can be triggered by hormones, was significantly downregulated in yeast-treated plants compared to untreated plants. Although the yeast-treated plants showed slightly improved hormone concentrations (IAA, ABA) in drought compared to untreated plants (IAA concentration increased approximately by 19 %), the action of <em>P. laurentii</em> was not likely connected to its ability to produce hormones, neither its ability to change the accumulation of proline. However, based on the oleaginous nature of <em>P. laurentii</em>, its positive influence on plants suffering from drought can be possibly explained by the production of fatty acids and their uptake by plants. This was supported by the increased concentration of fatty acids, especially in the roots of the yeast-treated plants (by 205.3 %).</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"44 ","pages":"Article 100542"},"PeriodicalIF":4.5,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933245","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}

{"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,&nbsp;Fatemeh Norouzi,&nbsp;Keramatollah Izadpanah,&nbsp;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}

{"title":"Approaches and challenges in machine learning for monitoring agricultural products and predicting plant physiological responses to biotic and abiotic stresses","authors":"Saeedeh Zarbakhsh ,&nbsp;Fazilat Fakhrzad ,&nbsp;Dragana Rajkovic ,&nbsp;Gniewko Niedbała ,&nbsp;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}

{"title":"Enhancing drought tolerance in Cannabis sativa L. by Trichoderma hamatum through optimized water usage","authors":"Byeong-Ryeol Ryu ,&nbsp;Gyeong-Ju Gim ,&nbsp;Ye-Rim Shin ,&nbsp;Min-Jun Kim ,&nbsp;Min-Ji Kang ,&nbsp;Tae-Hyung Kwon ,&nbsp;Sang-Hyuck Park ,&nbsp;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}

{"title":"The carotenoid biosynthesis pathway revealed to respond to Na2SiO3 stress on cotton growth","authors":"Ruize Song ,&nbsp;Xiao Chen ,&nbsp;Yunxin He ,&nbsp;Xuke Lu ,&nbsp;Hao Lan ,&nbsp;Yapeng Fan ,&nbsp;Hui Huang ,&nbsp;Yuping Sun ,&nbsp;Menghao Zhang ,&nbsp;Lidong Wang ,&nbsp;Fange Wu ,&nbsp;Xinrui Zhang ,&nbsp;Xin Yu ,&nbsp;Jie Jiang ,&nbsp;Shuai Wang ,&nbsp;Xiugui Chen ,&nbsp;Junjuan Wang ,&nbsp;Lixue Guo ,&nbsp;Lanjie Zhao ,&nbsp;Ling Li ,&nbsp;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 (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.</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}

{"title":"Metabolomic and transcriptomic analysis reveals high light to promote tuber enlargement through starch accumulation in Pinellia ternata","authors":"Duan Wu,&nbsp;Qin Chang,&nbsp;Minting Lu,&nbsp;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}

{"title":"Genome wide association mapping reveals genetic loci and candidate genes for seedling stage drought tolerance in lentil (Lens culinaris)","authors":"Neteti Siddartha Kumar ,&nbsp;Renu Pandey ,&nbsp;Anjali Anand ,&nbsp;Amit Kumar Singh ,&nbsp;Muraleedhar S. Aski ,&nbsp;Gyan Prakash Mishra ,&nbsp;Harsh Kumar Dikshit ,&nbsp;Mahesh Rao ,&nbsp;R.S. Bana ,&nbsp;Shiv Kumar ,&nbsp;Viswanathan Chinnusamy ,&nbsp;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 (&lt;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}

{"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 ,&nbsp;Ting Xiang Neik ,&nbsp;Ethan Tze Cherng Lim ,&nbsp;Adrian Ming Jern Lee ,&nbsp;Yi Lin Lim ,&nbsp;Wan Zu Tang ,&nbsp;Shuang Song ,&nbsp;Pei-Wen Ong ,&nbsp;Sin Joe Ng ,&nbsp;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}

{"title":"Decoding stress specific transcriptional regulation by causality aware Graph-Transformer deep learning","authors":"Umesh Bhati ,&nbsp;Akanksha Sharma ,&nbsp;Sagar Gupta ,&nbsp;Anchit Kumar ,&nbsp;Upendra Kumar Pradhan ,&nbsp;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}