Current Plant Biology最新文献

{"title":"Transcriptome signature for multiple biotic and abiotic stress in barley (Hordeum vulgare L.) identifies using machine learning approach","authors":"Bahman Panahi","doi":"10.1016/j.cpb.2024.100416","DOIUrl":"10.1016/j.cpb.2024.100416","url":null,"abstract":"<div><div>Barley (<em>Hordeum vulgare</em> L.) is exposed to various biotic and abiotic stresses, making it crucial to fully understand the gene signatures that respond to stress. This study utilizes machine learning to analyze transcriptomic data from 515 RNA-seq profiles across 18 independent studies, covering eleven abiotic and three biotic stress types. Through meticulous data preprocessing, including quality assessment and batch effect correction, we have identified 4311 genes for further analysis. Feature selection was performed using five weighting algorithms, resulting in the prioritization of 400 core genes. Machine learning models, specifically Random Forest and C4.5, were optimized and evaluated using a 10-fold cross-validation approach. The C4.5 algorithm demonstrated superior accuracy in predicting stress-responsive signatures. Key genes, such as bHLH119 and E3 ubiquitin protein ligase DRIP2, were identified as potential biomarkers. Functional enrichment analysis, conducted through protein-protein interaction networks and Gene Ontology/KEGG pathway analysis, has revealed significant involvement in lipid biosynthesis, signal transduction, and defense response processes. These findings highlight the crucial roles of the identified biomarkers genes in barley's resilience to stress and provide potential targets for genetic improvement. Future research should focus on validating these biomarkers in different barley cultivars and under field conditions to enhance crop resilience against stressors.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100416"},"PeriodicalIF":5.4,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142655932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated transcriptomic and metabolomic analysis reveals the effects of forchlorfenuron and thidiazuron on flavonoid biosynthesis in table grape skins","authors":"Ting Zheng ,&nbsp;Pengcheng Zhao ,&nbsp;Jiang Xiang ,&nbsp;Lingzhu Wei ,&nbsp;Wanting Shen ,&nbsp;Jiang Wu ,&nbsp;Jianhui Cheng","doi":"10.1016/j.cpb.2024.100417","DOIUrl":"10.1016/j.cpb.2024.100417","url":null,"abstract":"<div><div>Forchlorfenuron (CPPU) and thidiazuron (TDZ) are the most commonly used plant growth regulators in grape production. However, their application can result in astringency and uneven fruit skin coloring, which are related to flavonoid metabolic pathway. Therefore, this study investigated the effects of CPPU and TDZ on flavonoid synthesis in ‘Tiangong Moyu’ grape. The swelling effect of TDZ was better than that of CPPU, with T5 (25 mg·L⁻¹ GA₃+2.5 mg·L⁻¹ TDZ applied at 100 % flowering and 25 mg·L⁻¹ GA₃+2.5 mg·L⁻¹ TDZ applied 15 d later) showing the best swelling effect. Both CPPU and TDZ increased flavonoid content, and CPPU accelerated coloring. Combined with transcriptome analysis, cluster analysis showed that treatments T3 (two CPPU applications) and T5 had the strongest correlation. T5 caused the greatest change in flavonoid biosynthesis pathway. Weighted gene co-expression network analysis (WGCNA) showed that MM.magenta was correlated with tannin and flavonoid contents. <em>GST23</em> was consistent with the mature fruit flavonoid contents. <em>WRKY57</em> and <em>MYB86</em> increased after CPPU and TDZ treatment, especially in T5. Metabolomic analysis showed that the smallest difference in composition occurred between T1 (control) and T4 (one TDZ application), and naringenin only showed differences in T1 vs T4 and T1 vs T5, with enrichment in the flavonoid biosynthesis pathway. Association analysis in the flavonoid synthesis pathway showed that catechin, dihydrokaempferol, and naringenin were associated. Catechin is closely related to <em>CHS17</em>, with higher levels in T2 (one CPPU application) and T3. The above results provide a theoretical basis for improving grape berry quality using plant growth regulators.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100417"},"PeriodicalIF":5.4,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142655930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking the biochemical and computational parameters of Ceropegia foetida: A scientific approach for functional bioactive compounds from a medicinal food plant","authors":"Fawaz Alheibshy ,&nbsp;Abdulwahab Alamri ,&nbsp;Saad Saeed Saad Alshahrani ,&nbsp;Ahmed Awadh Saleh Alamri ,&nbsp;Nasser A.Awadh Ali ,&nbsp;Abdulwali Al-Khulaidi ,&nbsp;Arshad Hussain ,&nbsp;Sirajudheen Anwar","doi":"10.1016/j.cpb.2024.100414","DOIUrl":"10.1016/j.cpb.2024.100414","url":null,"abstract":"<div><div>Investigating the therapeutic potentials of medicinal plants remains pivotal in the discovery of novel bioactive compounds for food and pharmaceutical applications. This research delves into the phytochemical composition and biological activities of <em>Ceropegia foetida's</em> methanol extract, employing comprehensive UHPLC-MS for secondary metabolites profiling. The study quantifies the extract's substantial phenolic (76.12 mg GAE/g) and flavonoid (21.58 mg QE/g) contents, revealing a promising correlation with robust antioxidant activities, as evidenced by notable ABTS, FRAP, and CUPRAC assay outcomes. Furthermore, the extract demonstrates significant inhibitory effects on key enzymes implicated in neurodegenerative disorders and diabetes, including acetylcholinesterase (3.56 mg GALAE/g), butyrylcholinesterase (2.91 mg GALAE/g), and tyrosinase (128.31 mg KAE/g). UHPLC-MS analysis confirms the presence of 39 distinct phytochemicals across six primary categories, affirming the extract's complex bioactive profile. In complement to experimental assays, computational analyses <em>via</em> molecular docking simulations provided insights into the interaction mechanisms of identified phytochemicals with the target enzymes. These simulations revealed a substantial binding affinity of the plant's constituents towards enzymes compared to standard inhibitors, highlighting the compounds responsible for C<em>. foetida</em>'s bioactivity. Such computational insights, alongside empirical data, suggest that <em>C. foetida</em> merits further exploration as a natural source of therapeutic agents. Overall, the efficacious enzyme inhibition, coupled with the identified phytochemical diversity, underscores the potential of <em>C. foetida</em> as a valuable natural resource for developing nutraceuticals and therapeutic agents. These findings support the further investigation of <em>C. foetida</em> for its applicability in enhancing health and treating chronic conditions.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100414"},"PeriodicalIF":5.4,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142655934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The dwarf & pale leaf mutation reduces chloroplast numbers, resulting in sugar depletion that inhibits leaf growth of maize seedlings","authors":"Hamada AbdElgawad ,&nbsp;Katrien Sprangers ,&nbsp;Sofie Thys ,&nbsp;Isabel Pintelon ,&nbsp;Bart Cuypers ,&nbsp;Mohamed A. El-Tayeb ,&nbsp;Clifford Weil ,&nbsp;Kris Laukens ,&nbsp;Gerrit T.S. Beemster","doi":"10.1016/j.cpb.2024.100409","DOIUrl":"10.1016/j.cpb.2024.100409","url":null,"abstract":"<div><div>Plant growth is ultimately driven by cell division and expansion, but how these processes are regulated to mediate a wide range of genotypic variation in organ size is still poorly understood. To address this, we screened an EMS maize mutant population to identify a new EMS maize dwarf mutant with small, pale-yellow leaves (<em>dpl</em>). The mutation was mapped to a region of 11.58 Mb at the 3’ end of chromosome 7. We identified Zm00001d022394 as a potential causal gene for the <em>dpl</em> phenotype, encoding a pentatricopeptide repeat-containing (PPR) family protein involved in chloroplast gene expression and function, explaining the pale color of <em>dpl</em>. Mature <em>dpl</em> leaves are thinner and shorter due to a reduced number of cells of approximately normal length. The chloroplasts of <em>dpl</em> are reduced in size and number, correlating with a decreased chlorophyll content, however chloroplast ultrastructure was not affected. Consistent with the reduced chlorophyll content photosynthetic rate of <em>dpl</em> were reduced by 50 % and a 30 reduction of Fv/Fm suggests photoinhibition. As a consequence, soluble and insoluble sugar levels are severely reduced throughout the leaf growth zone. At the cell level reduced cell division rates and size of the division zone, explain the reduced leaf elongation rate (LER). The growth of <em>dpl</em> leaves can be restored by supplying growing leaves with sucrose through their cut tips, which also restores sucrose levels in the division zone of maize leaf, demonstrating that limited sugar availability explains the reduced growth phenotype. Inversely, we phenocopied the mutant growth phenotype by inhibiting photosynthetic electron transport in wild type plants with DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea). Our study of <em>dpl</em> provides a functional link between inhibition of photosynthesis, soluble sugar flux to the leaf growth zone, the regulation of cell division and whole leaf growth.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100409"},"PeriodicalIF":5.4,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142655931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long non-coding RNAs: A promising tool to improve horticultural quality traits","authors":"Ahmed Alabd ,&nbsp;Junbei Ni ,&nbsp;Xuxu Wang ,&nbsp;Songling Bai ,&nbsp;Yuanwen Teng","doi":"10.1016/j.cpb.2024.100413","DOIUrl":"10.1016/j.cpb.2024.100413","url":null,"abstract":"<div><div>Horticultural crops, including fruits, vegetables, and ornamental plants, are important agricultural commodities with high economic value. They are cultivated for food, specific nutrition, and medical proposes. Long non-coding RNAs (lncRNAs), a large class of non-coding RNAs, play a central role in regulating diverse developmental and physiological processes. Recently, high-throughput sequencing has enabled the identification of plant lncRNAs engaged in regulating the quality traits of horticultural crops. Here, we provide a brief overview of the lncRNAs biogenesis, classification, characteristics and localization of lncRNAs. Furthermore, we present a propos workflow for the identification and functional investigation of plant lncRNAs. Subsequently, we examine studies that elucidate the function of lncRNAs in regulating quality traits in diverse horticultural crops, thereby enhancing our understanding of the mechanisms by which lncRNAs regulate quality trait improvements. In the future, it will be necessary to gain a deeper understanding of the molecular mechanisms underlying lncRNA-mediated quality development in horticultural crops. It is our contention that future studies on lncRNA will provide effective approaches for the improvement of horticultural crops, thereby ensuring global food security.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100413"},"PeriodicalIF":5.4,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142655929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using next-generation sequencing approach for discovery and characterization of plant molecular markers","authors":"Bahman Panahi ,&nbsp;Hossein Mohammadzadeh Jalaly ,&nbsp;Rasmieh Hamid","doi":"10.1016/j.cpb.2024.100412","DOIUrl":"10.1016/j.cpb.2024.100412","url":null,"abstract":"<div><div>Crop development is critical to meeting the world's growing food needs, especially in light of the challenges posed by climate change and population growth. Molecular markers (MM) have become an indispensable tool in breeding programmes as they enable rapid trait selection and monitoring of genetic variation. Next generation sequencing (NGS) has transformed genomics by providing low-cost, high-throughput technologies for the identification of markers in plants. This review focuses on the latest applications, advances and opportunities of NGS in the discovery and characterization of MM in plants. We have addressed the involvement of NGS in the detection of different types of markers such as single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) and structural variants (SVs) and their applications in functional genomics and plant breeding. We have also demonstrated the possibility of combining NGS with modern bioinformatics techniques to accelerate the development of markers and improve crop resistance and yield.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100412"},"PeriodicalIF":5.4,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142656020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The simultaneous application of fulvic acid and protein hydrolysate biostimulants enhances cucumber responses to Fe deficiency","authors":"Giacomo Rodegher ,&nbsp;Stefano Ambrosini ,&nbsp;Tiziana Pandolfini ,&nbsp;Serena Zanzoni ,&nbsp;Anita Zamboni ,&nbsp;Zeno Varanini","doi":"10.1016/j.cpb.2024.100411","DOIUrl":"10.1016/j.cpb.2024.100411","url":null,"abstract":"<div><div>Iron (Fe) is widely recognized as a critical factor in limiting crop production; however, eco-friendly strategies to address its deficiency are still required. The use of biostimulants has displayed promising results in mitigating Fe deficiency. Our hypothesis was that the combined application of two biostimulants with distinct molecular structures - fulvic acid (FA) and protein hydrolysate (PH) - could be more effective than the use of a single compound. The simultaneous presence of FA and PH (MIX) in a Fe-free nutrient solution led to a redistribution of endogenous Fe, resulting in a higher leaf SPAD index. Furthermore, the addition of FeCl₃ as a Fe source (resupply) in MIX-treated plants enhanced the biostimulant effect, as evidenced by increased dry root and shoot weight and a more developed root system. In addition, the expression of Strategy-I-related genes, <em>CsFRO1</em> and <em>CsIRT1</em>, remained elevated. These effects can be attributed to improved interaction between the roots and biostimulants through the formation of the FA-PH complex, as demonstrated by circular dichroism and isothermal titration calorimetry analyses.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100411"},"PeriodicalIF":5.4,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142656152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of biostimulants on the chemical profile of food crops under normal and abiotic stress conditions","authors":"Salima Boutahiri,&nbsp;Rachid Benrkia,&nbsp;Babalwa Tembeni,&nbsp;Olusola Emmanuel Idowu,&nbsp;Opeyemi Joshua Olatunji","doi":"10.1016/j.cpb.2024.100410","DOIUrl":"10.1016/j.cpb.2024.100410","url":null,"abstract":"<div><div>Biostimulants are substances/micro-organisms that have the ability to stimulate plant growth, nutrition and stress tolerance independently of their nutritional content. They are increasingly replacing the use of chemical fertilizers, which have harmful consequences for the environment. Biostimulants are derived from a variety of sources, including micro-organisms, plant extracts, algae, hydrolysates of animal or plant proteins, and humic substances. They have been tested on a variety of crops under normal and abiotic stress conditions and have succeed each time in proving their effectiveness in improving the chemical composition of plants. This improvement has a positive impact on plants' nutritional properties and resistance to stress conditions. These effects not only have positive impact on human health, but also on climate change challenges, and increasing demand for food. However, the difficulty in interpreting the results obtained from the use of biostimulants is due to their variable composition, which is not always known, making it difficult to determine their modes of action and hence their regulation. The purpose of this review is to highlight the positive effect of biostimulants on the chemical composition of food crops under normal or abiotic stress conditions. It presents an overview of chemical variability in plants and gathers studies that help clarify the effect of biostimulants. Additional studies on economic aspects, research gaps, and future prospects in the field of biostimulants are also discussed.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100410"},"PeriodicalIF":5.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetic control of plant regeneration: Unraveling the role of histone methylation","authors":"Saikat Sena ,&nbsp;Ajit Prakash ,&nbsp;Johannes Van Staden ,&nbsp;Vijay Kumar","doi":"10.1016/j.cpb.2024.100408","DOIUrl":"10.1016/j.cpb.2024.100408","url":null,"abstract":"<div><div>It is incredible that plants can actively promote cellular dedifferentiation and regeneration. The change in cell fate is accompanied by modifications to the epigenetic landscape. Plants may regulate developmental processes and environmental adaptation via the establishment, maintenance, and removal of epigenetic changes in addition to genetically encoded variables. Studies on plant regeneration are very important since the underlying processes are connected to basic research in many different domains as well as the development of widely used plant biotechnology. <em>De novo</em> organogenesis, somatic embryogenesis, and tissue regeneration are the three primary kinds of regeneration observed in higher plants. <em>In-vitro</em> culturing may cause histone methylation to reassemble the nuclear architecture. The process of somatic embryogenesis and regeneration relates to different methylation states that regulate gene expression <em>in-vitro</em>. In order to generate huge amounts of top-notch planting materials or to enhance agronomic features that promote crop development, it may be necessary to change the methylation profile. Enhancing the embryogenic potential and totipotency in resistant plant species and specific genotypes could be achievable by developing techniques with the aid of an understanding of the molecular processes behind methylation changes and the acquisition of embryonic cell destiny during <em>in-vitro</em> cultures. Additionally, the methylation profile may help crops adapt to extreme conditions when they experience diverse challenges throughout <em>in-vitro</em> growth. In this article, we examine the studies on how histone methylation affects plant variety and explore the possibilities of targeted epigenetic modification for crop development.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100408"},"PeriodicalIF":5.4,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142656153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sustainable nitrogen solutions: Cyanobacteria-powered plant biotechnology for conservation and metabolite production","authors":"Taufiq Nawaz ,&nbsp;Shah Fahad ,&nbsp;Shah Saud ,&nbsp;Ruanbao Zhou ,&nbsp;Nader R. Abdelsalam ,&nbsp;Mohamed M.A. Abdelhamid ,&nbsp;Mariusz Jaremko","doi":"10.1016/j.cpb.2024.100399","DOIUrl":"10.1016/j.cpb.2024.100399","url":null,"abstract":"<div><div>As photosynthetic microorganisms, cyanobacteria play a dominant part in numerous ecological systems owing to their ability to fix carbon and nitrogen and are therefore an essential part of primary production in both aquatic and terrestrial environments. The utility of nitrogen-fixing cyanobacteria in plant biotechnology opens up promising strategies for the conservation and sustainable use of rare, endangered plant species and bioactive cell cultures. Here, we discuss the complicated physiological aspects of biological nitrogen fixation in cyanobacteria and their symbiotic relationship with plants. This review focuses on recent advances in biotechnological tools such as CRISPR-Cas9, nanotechnology and multiomics-based approaches for enhancing plant regeneration systems to cultivate specialized metabolites. We also look at the methods in vitro preservation of plants and how to scale up a culture using bioreactor systems. The review ends by highlighting the promise of cyanobacteria-powered plant biotechnology as a renewable mechanism for rare species conservation and specialized metabolites production, providing an optimistic modal, formative future direction in plant biosynthesis.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"40 ","pages":"Article 100399"},"PeriodicalIF":5.4,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142539537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}