Alejandra E. Melgar , Axel J. Rizzo , Laura Moyano , Rocío Cenizo , María B. Palacios , Alicia M. Zelada
{"title":"Genome-wide identification and salt stress-expression analysis of the dehydrin gene family in Chenopodium quinoa","authors":"Alejandra E. Melgar , Axel J. Rizzo , Laura Moyano , Rocío Cenizo , María B. Palacios , Alicia M. Zelada","doi":"10.1016/j.cpb.2024.100340","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100340","url":null,"abstract":"<div><p>Dehydrins (DHNs) are essential proteins in the embryonic development and abiotic stress responses of plants. Due to their remarkable ability to confer tolerance to plants in conditions of drought, salinity and extreme temperatures, DHNs have garnered considerable interest. Quinoa (<em>Chenopodium quinoa</em> Willd.), a facultative halophyte plant, can thrive in a wide range of agroecosystems, making it a promising candidate for stress tolerance studies. In this study, we identified eleven DHN genes in the quinoa genome belonging to Y-, F- and H-orthologous groups found in angiosperms. Notably, the H-DHNs lack the K-segment, a feature observed in all Amaranthaceae species, but not in other angiosperms. We identified four DHN structural subgroups: FSKn, YnSKn, SKn-DHNs and the atypical HS-DHN. Phylogenetic analysis indicated that each structural subgroup, except for SK2-DHN, presents two paralogous genes, in accordance with the allotetraploid character of <em>C. quinoa</em>. Quantitative real-time PCR expression analysis revealed that DHN1s (FSK2) and DHN3s (Y2SK2) were expressed in all tissues, while DHN2s (FSK3) were predominant in roots and DHN4s (Y4SK2 and SK2) were predominant in flowers. Salt-response gene expression analysis in seedlings showed that CqDHN4s increase their expression in response to salt stress in all varieties studied, while CqDHN1s reduce their expression in a more salt stress-tolerant variety, suggesting a possible adaptive advantage. <em>In silico</em> analysis of the promoters of CqDHN1s and CqDHN4s supports the involvement of these DHNs in responding to abiotic stress.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100340"},"PeriodicalIF":5.4,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000227/pdfft?md5=726d86edc3215f75f456dffee1bd795e&pid=1-s2.0-S2214662824000227-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140347897","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":"Traditional and next-generation methods for browning control in plant tissue culture: Current insights and future directions","authors":"Nandang Permadi , Sulistya Ika Akbari , Dedat Prismantoro , Nastiti Nur Indriyani , Mohamad Nurzaman , Arshad Naji Alhasnawi , Febri Doni , Euis Julaeha","doi":"10.1016/j.cpb.2024.100339","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100339","url":null,"abstract":"<div><p>Plant tissue culture plays a central role in the agricultural, horticultural, research, and conservation sectors. It facilitates precise control over plant propagation and manipulation, resulting in enhanced crop yields, effective disease management, and the preservation of endangered plant species. Browning, a well-acknowledged limitation in plant tissue culture, poses potential challenges to successful in vitro plant multiplication. Browning primarily occurs in response to enzymatic reactions due to explant damage. Left untreated, it can lead to a reduced in the regeneration capacity, hindered callus proliferation, impeded development of adventitious shoots, and, in extreme cases, tissue necrosis. To mitigate the issue of browning, several in vitro strategies have been implemented i.e., submerging the explants in specialized solutions designed to inhibit browning, incorporating anti-browning agents into the growth medium, and adhering to certain cultural techniques. This article aims to comprehensively examine the factors contributing to browning and the multitude of strategies employed to effectively manage browning problems in plant tissue cultures. Furthermore, it explores the potential of encapsulating natural products as a cutting-edge method for addressing browning in plant tissue culture. These innovative approaches offer promising avenues for controlling browning in plant tissue culture, thereby contributing to the advancement of sustainable agricultural practices and conservation efforts.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100339"},"PeriodicalIF":5.4,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000215/pdfft?md5=878d259aa61c77f3d088d88c612d473b&pid=1-s2.0-S2214662824000215-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140350594","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":"Metabolomic characterization of alkali stress responses in rice","authors":"Ryoma Kawakami , Masataka Wakayama , Tetsuo Takano , Shenkui Liu , Keisuke Nemoto","doi":"10.1016/j.cpb.2024.100337","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100337","url":null,"abstract":"<div><p>Soil alkalinity due to the accumulation of alkaline salts greatly impairs crop production. Despite advancements in crop stress response studies through metabolomic analyses, limited progress has been made in understanding cultivar differences in alkali tolerance due to the scarcity of suitable genetic material. This study aimed to characterize the metabolic responses to alkali stress in two rice cultivars, Kasalath (alkali-sensitive) and Gharib (alkali-tolerant), which were screened in an alkali soil field. A metabolomic analysis of the responses of hydroponically grown seedlings of both cultivars to alkaline and neutral salt stress was performed. Under alkali stress, the tolerant cultivar Gharib showed a significant accumulation of metabolites from the TCA organic acid and arginine synthesis pathways. This accumulation is consistent with observations in alkaliphilic wild grasses and may account for the superior alkali tolerance of Gharib. Although amino acids and nitrogen-containing metabolites, such as asparagine and allantoin, also accumulated under alkali stress, their accumulation was not specific to alkali stress, as previously reported. They accumulated similarly in both Kasalath and Gharib, suggesting that while these metabolites may alleviate alkali stress, they are unlikely to be responsible for cultivar differences in rice alkali tolerance.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100337"},"PeriodicalIF":5.4,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000197/pdfft?md5=b196955418981e62304774f4726369a9&pid=1-s2.0-S2214662824000197-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140138400","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":"Identification and characterization of novel drought-responsive lncRNAs in stone apple (Aegle marmelos L.) through whole-transcriptome analysis","authors":"Kishor U. Tribhuvan , Twinkle Mishra , Simardeep Kaur , Avinash Pandey , Shashi Bhushan Choudhary , V.P. Bhadana , Sujay Rakshit , Binay K. Singh","doi":"10.1016/j.cpb.2024.100336","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100336","url":null,"abstract":"<div><p>Stone apple (<em>Aegle marmelos</em> L.) is a subtropical fruit tree of the Rutaceae family, highly valued in traditional medicine across the Indian subcontinent. We conceived this study with the objective of developing a comprehensive transcriptome dataset, identifying SSRs for marker-assisted breeding, and delineating regulators of gene expression, with a specific emphasis on non-coding RNA (ncRNA), particularly related to drought stress. To achieve this, RNA-seq was conducted using RNA pooled from various tissues, including roots, leaves, inflorescence, and developing seeds from stone apple, and the clean reads were assembled into 40,886 unigenes. Subsequently, the unigenes were categorized into gene ontology categories encompassing biological processes, molecular functions, and cellular components. Within the unigenes, we identified a total of 9174 perfect simple sequence repeats (SSRs), 2167 transcription factors (TFs) distributed among 69 families, and 415 transcription regulators (TRs) across 27 families. Additionally, 19 microRNAs (miRNAs) from 12 families, 16,811 potential long noncoding RNAs (lncRNAs), and six functional endogenous target mimics (eTMs) were detected. Analysis of lncRNA-miRNA-mRNA interactions unveiled multiple regulatory nodes, elucidating lncRNA/miRNA-driven gene expression control in stone apple. The increased co-expression of selected drought-related lncRNAs and their cognate target mRNAs supported the aforementioned findings under drought conditions. Overall, this study significantly advances our understanding of stone apple genomics and lays a foundation for future omics-based studies, thereby facilitating the deployment of climate-resilient strategies in the species.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100336"},"PeriodicalIF":5.4,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000185/pdfft?md5=b56bf64083689fa09ad36e39c513c9b7&pid=1-s2.0-S2214662824000185-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140052273","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":"Unveiling the role of vermicompost in modulating phenylpropanoid metabolism in basil (Ocimum basilicum L.): A single-cell type PGT approach","authors":"İlker TÜRKAY , Lokman ÖZTÜRK , Fevziye Şüheda HEPŞEN TÜRKAY","doi":"10.1016/j.cpb.2024.100335","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100335","url":null,"abstract":"<div><p>This research delves into phenylpropanoid metabolism, focusing on phenylpropene biosynthesis in the methyleugenol chemotype of basil (<em>Ocimum basilicum</em> L.). We isolated peltate glandular trichomes (PGTs) from basil leaves to eliminate primary metabolic influences, offering a unique perspective into these complex processes. Vermicompost, chosen for its eco-friendly composition and superiority in invigorating phenylpropanoid metabolism. In this study, we investigated the impacts of solid and tea-form vermicompost applications at 0%, 10%, and 25% doses on the methyleugenol chemotype of basil, focusing on the expression levels of <em>PAL</em>, <em>4CL</em>, <em>EGS</em>, <em>EOMT</em>, and <em>CVOMT</em> genes and phenylpropene accumulation in the peltate glandular trichomes. Results showed that 10% solid vermicompost (SV) application increased <em>4CL</em> expression level at 236%, while 25% SV application further enhanced <em>EOMT</em> and <em>CVOMT</em> expressions to towering values by 7,494-fold and 19,643-fold, respectively. SV applications did not significantly impact eugenol accumulation but suppressed chavicol biosynthesis. Methyleugenol and methylchavicol accumulation rose in a dose-dependent manner, with significant increases observed in the 25% SV application. A positive correlation was found between <em>CVOMT</em> expression and accumulation rates of methyleugenol and methylchavicol phenylpropenes following SV applications. Conversely, vermicompost tea (VT) applications led to mixed gene expression patterns and reduced eugenol and methyleugenol ratios in peltate glandular trichomes compared to control. In summary, the notably high gene expressions observed in the results of our preliminary study offer a new perspective in the field of phenylpropanoid metabolism. This underscores the value of utilizing single-cell type PGTs for examining secondary metabolic pathways in plants and demonstrates the impact of vermicompost on phenylpropene production.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100335"},"PeriodicalIF":5.4,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000173/pdfft?md5=2175869e5669cd725e0be3af99d9f749&pid=1-s2.0-S2214662824000173-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140095890","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":"Transcriptome-wide characterization of alternative splicing regulation in Najran wheat (Triticum aestivum) under salt stress","authors":"Norah Alyahya , Tahar Taybi","doi":"10.1016/j.cpb.2024.100334","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100334","url":null,"abstract":"<div><p>The process of alternative splicing (AS) has emerged as a crucial mechanism in plant responses to environmental stresses, contributing to the enhancement of the required transcriptome and proteome complexity. Despite the importance of AS, there remains a paucity of studies on the regulatory implications of AS in the responses of wheat to salt stress. In the current study, transcriptome-wide changes in AS profiles were established in roots and shoots of Najran wheat treated with 200 mM NaCl. Salt stress induced AS events increasing the complexity of the transcriptome; out of all expressed genes in all samples, 32,268 genes (22.5% of expressed genes) in the roots and 31,941 genes (23.1% of expressed genes) in the shoots were subjected to AS with 3’ Alternative splice site (A3) being the most frequent AS event and mutually exclusive exon (MX) being the least common event. Moreover, the results revealed that salt stress modulates AS patterns in a tissue-specific way where 82% of AS events were differentially expressed in either root or shoot tissues, participating in organ differentiation. In Total, 423 Differential AS events associated with cytoskeletal-related categories such as microtubule-based processes, actin filament-based movements, and cytoskeletal motor activity were identified in the roots. In contrast, 393 Differential AS events associated with biological categories related to metabolic and signalling processes such as catabolic processes, and response to gibberellin were identified in the shoots. The results presented in this study enhance our understanding of salt tolerance mechanisms in wheat and provide promising insights for future functional investigations and crop improvement efforts.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100334"},"PeriodicalIF":5.4,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000161/pdfft?md5=8e757a5b05da37b950e1904ee5df2d4a&pid=1-s2.0-S2214662824000161-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139999722","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}
Aline Marengoni Almeida , Diany Lucy Silveira dos Reis , Eduardo Jorge Pilau , Rogério Barbosa de Lima , Rodrigo Polimeni Constantin , Rogério Marchiosi , Osvaldo Ferrarese-Filho , Wanderley Dantas dos Santos
{"title":"Soybean and maize differentially metabolize deuterated ferulic and sinapic acids before polymerizing them into the root cell wall","authors":"Aline Marengoni Almeida , Diany Lucy Silveira dos Reis , Eduardo Jorge Pilau , Rogério Barbosa de Lima , Rodrigo Polimeni Constantin , Rogério Marchiosi , Osvaldo Ferrarese-Filho , Wanderley Dantas dos Santos","doi":"10.1016/j.cpb.2024.100333","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100333","url":null,"abstract":"<div><p>Hydroxycinnamates induce lignification in young plants, leading to the overproduction of lignin as a defense mechanism. Phenylpropanoids-containing oligosaccharides are thought to be a signal of pathogen attack on the cell wall polysaccharides. However, it is unclear if hydroxycinnamates induce lignification by acting solely as stress elicitors or feeding the phenylpropanoid pathway as lignin precursors. To examine this hypothesis, we added 1 mM deuterated ferulic acid (FA) or sinapic acid (SA) to the nutrient solution in which we cultivated soybean or maize plantlets. After 24 h, we assessed the biometric parameters and the contents of ester-linked FA and SA, total lignin, monolignol ratio, and heavy monolignols. FA treatment increased the content of ester-linked FA, syringyl, and guaiacyl monomers measured by nitrobenzene oxidation, lignin content, and reduced root growth in both soybean and maize plants. <em>p</em>-Coumaric acid content ester-linked to the cell wall increased in soybean but decreased in maize after treatment with FA. Treatment with SA also induced lignification in soybean but not in maize. SA increased S-lignin and sinapoyl esters content in the cell wall polymers in both soybean and maize. Residues of deuterated hydroxycinnamates were detected in the lignin of both plants in both treatments. The assay demonstrated that exogenously applied SA and FA were metabolized through the phenylpropanoid pathway. Furthermore, they were, at least partially, exported to the apoplast, where they were ester-linked to cell wall polymers. This suggests hydroxycinnamic acids are metabolized differently by plants with different types of cell walls.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100333"},"PeriodicalIF":5.4,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S221466282400015X/pdfft?md5=c0036600a7cb6ed35c3ff1f6bf2462d7&pid=1-s2.0-S221466282400015X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140015359","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}
Ian Paul Navea , Shiyi Yang , Priskila Tolangi , Raña Mae Sumabat , Wenhua Zhang , Joong Hyoun Chin
{"title":"Enhancement of rice traits for the maintenance of the phosphorus balance between rice plants and the soil","authors":"Ian Paul Navea , Shiyi Yang , Priskila Tolangi , Raña Mae Sumabat , Wenhua Zhang , Joong Hyoun Chin","doi":"10.1016/j.cpb.2024.100332","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100332","url":null,"abstract":"<div><p>Phosphorus (P) is essential for maximizing crop yield, yet many areas dedicated to rice cultivation suffer from a scarcity of plant-accessible inorganic phosphate (Pi) due to its fixation in the soil. Conversely, regions with ample P fertilization often resort to excessive application to compensate for deficiencies, resulting in adverse environmental impacts. While significant strides have been made in understanding the molecular mechanisms governing P uptake capacity (PUP/PAE) and P use efficiency (PUE) in rice, their practical implementation in breeding is impeded by the absence of robust, high throughput phenomics techniques, leading to inconsistencies in gene/quantitative trait loci (QTL) effects. This review underscores the necessity for a comprehensive understanding of Pi transporters, internal Pi remobilization, and root morphology modifications under Pi deficiency, correlating these traits with specific phenotypic markers. Developing precise, cost-effective, high-throughput phenotyping techniques is imperative for creating rice ideotypes with enhanced PAE/PUE. Additionally, we explore the potential of meta-QTL analysis in prioritizing genomic loci related to PUE, utilizing a “meta-genome” encompassing diverse rice reference genomes. We also delve into the potential in the development of phosphite (Phi)-tolerant rice, aiming to reduce dependence on P fertilizers and create herbicide-resistant rice through Phi-based fertilization. Finally, we discuss the utilization of arbuscular mycorrhizal fungi (AMF) to enhance P uptake in rice.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100332"},"PeriodicalIF":5.4,"publicationDate":"2024-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000148/pdfft?md5=00cb37aa0a08182e97eb8a5c688a03b1&pid=1-s2.0-S2214662824000148-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139992597","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":"Functional phenotyping: Understanding the dynamic response of plants to drought stress","authors":"Sheikh Mansoor, Yong Suk Chung","doi":"10.1016/j.cpb.2024.100331","DOIUrl":"https://doi.org/10.1016/j.cpb.2024.100331","url":null,"abstract":"<div><p>Drought stress, exacerbated by climate change, presents a critical global challenge characterized by increasingly severe and prolonged dehydration events. This phenomenon poses significant obstacles to both agricultural productivity and ecological stability. One promising strategy for addressing this issue involves functional phenotyping, a methodology that provides invaluable insights into the intricate responses of plants to water scarcity. A profound understanding of these responses is crucial for the advancement of drought-tolerant crop cultivars/species, the optimization of irrigation methodologies, and the implementation of effective water resource management practices in agriculture. This review underscores the potential of developing an ideal phenotyping tool that continuously monitors a plant's physiological profile in response to shifting environmental parameters. Such an approach enables the multifaceted characterization and assessment of various functional phenotypes and productivity levels. Through the application of functional phenotyping techniques, we stand to gain invaluable insights into plant behaviour, thereby contributing to the development of drought-tolerant crops and the establishment of sustainable agricultural systems.</p></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"38 ","pages":"Article 100331"},"PeriodicalIF":5.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214662824000136/pdfft?md5=c8ca3e47242ab21fc6be275b445bfe29&pid=1-s2.0-S2214662824000136-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139945024","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}