TreesPub Date : 2025-10-18DOI: 10.1007/s00468-025-02692-0
Hans Pretzsch, Astor Toraño Caicoya, Miren del Río
{"title":"Estimating tree age depending on tree height for Norway spruce, Scots pine, European beech, and sessile and common oak in Central Europe","authors":"Hans Pretzsch, Astor Toraño Caicoya, Miren del Río","doi":"10.1007/s00468-025-02692-0","DOIUrl":"10.1007/s00468-025-02692-0","url":null,"abstract":"<div><p>The age of trees in forests, open land, or urban areas is important for biodiversity monitoring, sustainable management, or hazard assessment; but it is often unknown. The height of trees, on the other hand, is often known from remote sensing or can be measured easily and non-destructively. However, there is a sigmoidal relationship between tree age and height, whose inverse function can be used to estimate age from height. Here, we compiled measurements of tree height and age from pre-dominant and dominant trees on long-term experimental plots for the parameterization of a density- and site index-dependent height-age function, tree height = <span>({text{f}}_{1})</span>(tree age, site index, stand density). The study focused on Norway spruce (<i>Picea abies</i> (L.) Karst.), Scots pine (<i>Pinus sylvestris</i> L.), European beech (<i>Fagus sylvatica</i> L.), and sessile and common oak (<i>Quercus robur</i> L. and <i>Quercus petraea</i> (Matt.) Liebl.) in Central Europe. The extended Chapman-Richard function was used and its inverse function tree age = <span>({text{f}}_{2})</span>(tree height, site index, SDI) enables age estimation from tree height. To quantify prediction uncertainty, a non-parametric bootstrap was applied to the inverted model, providing height-dependent 95% confidence intervals that account for both parameter variability and the non-linearity of the inversion. The accuracy of the age estimation was higher for low and medium height trees (<span>(11-21%)</span>) and decreased with tree height (<span>(14-22%)</span>), a pattern confirmed by the bootstrap-derived confidence intervals. We discussed the application possibilities and limitations of the functions for estimating tree age in the context of monitoring, inventory, evaluation or management of forests or urban trees.</p></div>","PeriodicalId":805,"journal":{"name":"Trees","volume":"39 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00468-025-02692-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145316295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kai Pi, Ting Liang, Qiwei Yu, Zhenbao Luo, Jiajun Luo, Lili Duan, Jingyao Zhang, Renxiang Liu
{"title":"NtDEAH1 Modulates Gibberellin Receptor NtGID1 Expression and Negatively Regulates Leaf Number in Tobacco.","authors":"Kai Pi, Ting Liang, Qiwei Yu, Zhenbao Luo, Jiajun Luo, Lili Duan, Jingyao Zhang, Renxiang Liu","doi":"10.1111/pce.70246","DOIUrl":"https://doi.org/10.1111/pce.70246","url":null,"abstract":"<p><p>Tobacco (Nicotiana tabacum L.) is a crop of major economic importance worldwide and also a widely used model in plant biology and genetics. Leaf number (LN) is a key agronomic trait that determines yield. To elucidate its genetic basis, we developed a mapping population by crossing the low-leaf, high-quality cultivar 'NC82' with the high-leaf cultivar 'Jiucaiping No.2' (JCP2). Bulked segregant analysis initially placed the locus controlling LN within a 6.16 Mb region on chromosome 9. The integration of competitive allele-specific PCR markers with RNA sequencing data narrowed down this region and identified a single candidate gene, NtDEAH1. Overexpression of NtDEAH1 in both NC82 and JCP2 backgrounds significantly reduced LN, whereas CRISPR/Cas9-mediated knockout increased LN, indicating that NtDEAH1 acts as a negative regulator of LN and is a previously unreported control factor. Transcriptomic profiling and phytohormone analyses revealed that NtDEAH1 modulates the expression of genes in the gibberellin pathway. Specifically, NtDEAH1 binds to the 5'-untranslated region of the gibberellin receptor gene NtGID1, thereby influencing mRNA stability and translational efficiency to regulate LN. These findings provide new insights into genetic and molecular mechanisms underlying LN determination, and suggest that NtDEAH1 may serve as a target for future breeding aimed at optimising plant architecture and enhancing yield.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.3,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Loss of CsCLV2 function causes dwarfism and determinates growth in cucumber","authors":"Lin Chen, Maomao Yun, Baoying Chen, Shuyan Xie, Wenrui Liu, Min Wang, Jinqiang Yan, Jinsen Cai, Songguang Yang, Qingwu Peng, Dasen Xie, Yu'e Lin, Biao Jiang","doi":"10.1111/tpj.70525","DOIUrl":"10.1111/tpj.70525","url":null,"abstract":"<div>\u0000 \u0000 <p>Cucumber (<i>Cucumis sativus</i> L.) is a globally important vegetable crop. Ideal plant architecture optimizes spatial utilization, enhances economic coefficient, and facilitates mechanized cultivation. In this study, we identified a dwarf mutant, <i>csdw3</i>, exhibiting reduced plant height, shortened internodes, and fewer internodes. Genetic analysis showed that this dwarf phenotype is controlled by a single recessive gene. Fine-mapping localized the causal locus to an 80 kb region on chromosome 1, where we discovered a 102 bp deletion in <i>CsCLV2</i>, a gene encoding a leucine-rich repeat receptor-like protein homologous to <i>Arabidopsis CLAVATA2</i>. CRISPR-Cas9-generated loss-of-function mutants recapitulated the dwarf phenotype, confirming the role of <i>CsCLV2</i> in plant height regulation. Histological examination revealed that <i>CsCLV2</i> disruption causes premature termination of shoot apical meristem (SAM) development, reducing both internode number and length. Protein interaction assays further demonstrated that <i>CsCLV2</i> associates with receptor-like kinase <i>CsCIK1</i> (<i>CLAVATA3 INSENSITIVE RECEPTOR KINASES 1</i>), indicating their cooperative function in the <i>CLV</i>-<i>WUS</i> signaling pathway to maintain meristem activity. Our findings uncover a regulator of plant height in cucumber and provide valuable genetic resources for breeding ideotypes optimized for yield and cultivation efficiency.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Promiscuous potatoes: the genetic basis of wild potato compatibility","authors":"Gwendolyn K. Kirschner","doi":"10.1111/tpj.70529","DOIUrl":"10.1111/tpj.70529","url":null,"abstract":"<p>Few plants have shaped dinner plates and world history quite like the potato. Both the tetraploid cultivated potato (<i>Solanum tuberosum</i> L.) and its wild tuber-bearing relatives belong phylogenetically to the <i>Solanum</i> section <i>Petota</i> (Yan et al., <span>2023</span>). There are more than 100 recognized species of cultivated potatoes and their wild relatives. Like cultivated potatoes, many of these carry the A genome; they are primarily found in South America and are reproductively isolated from Mexican diploid species. The only diploid A-genome species occurring in Mexico is <i>Solanum verrucosum</i> Schlechtendal, which also serves as a maternal ancestor of Mexican polyploid species (Hosaka et al., <span>2022</span>). Interestingly, <i>S. verrucosum</i> is also the only A-genome diploid potato species that is fully self-compatible.</p><p>William Behling, first author of the highlighted publication, has long been fascinated by crop wild relatives, and he was especially drawn to <i>S. verrucosum</i>, which can serve as a bridge between the gene pool of cultivated and wild species because it can be fertilized by a broad range of wild <i>Solanum</i> species (Behling et al., <span>2024</span>). The more he worked with <i>S. verrucosum</i>, the more he wanted to know why this species was able to do something that no other potato species seemed to be able to do—accept pollen from any male-fertile pollen donor.</p><p>In <i>S. verrucosum</i>, self-compatibility has been attributed to the lack of S-ribonuclease (S-RNase) expression in the style (Eijlander et al., <span>2000</span>). Together with other factors such as HT genes, the S-RNase has a cytotoxic effect on incompatible pollen tubes penetrating the style. However, knocking out the <i>S-RNase</i> gene in <i>S. tuberosum</i> is not sufficient to replicate the phenotypes observed in <i>S. verrucosum</i> (Behling & Douches, <span>2023</span>). Additionally, there are examples of pollen rejection mechanisms that are independent of S-RNase in interspecific pollinations in tomato (Tovar-Méndez et al., <span>2017</span>). Therefore, Behling, David Douches and colleagues set out to identify additional genetic factors that determine interspecific compatibility in <i>S. verrucosum</i> (Behling et al., <span>2025</span>).</p><p>To create a F2 mapping population, segregating for the presence and absence of interspecific reproductive barriers (IRBs), the authors selected two <i>Solanum</i> parents differing in their reproductive behaviour: DM1S1, a <i>S. tuberosum</i> doubled monoploid that is effectively male sterile and has functional IRBs, but is able to accept pollen from <i>S. verrucosum</i>; and MSJJ1813-2, a <i>S. verrucosum</i> clonal selection that exhibits a high degree of male fertility, self-compatibility and lacks IRBs (Figure 1a).</p><p>To test for self-compatibility, the population was then allowed to self-pollinate. The authors first classified the phenotypes as self-compat","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70529","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mycorrhizal Type and Soil Nitrogen Content Coregulate Foliar Nutrient Responses to Neighborhood Functional Dissimilarity in Subtropical Forests.","authors":"Xue Zhao, Zhihong Xu, Fulin Chen, Tao Wang, Qingyong Lin, Zaipeng Yu, Zhichao Xia, Linfeng Li, Zhiqun Huang","doi":"10.1111/pce.70243","DOIUrl":"https://doi.org/10.1111/pce.70243","url":null,"abstract":"<p><p>Foliar nitrogen (N) and phosphorus (P) concentrations are of critical importance to plant productivity. Despite global declines in plant diversity, their effects on tree foliar N and P dynamics remain uncertain, especially under different mycorrhizal types and soil nutrient conditions. Based on a large biodiversity experiment in subtropical China, we assessed how neighborhood species richness and functional dissimilarity influence foliar N and P concentrations across 794 tree individuals, comprising three arbuscular mycorrhizal (AM) and five ectomycorrhizal (EcM) tree species, along natural soil total N gradients. At the neighborhood scale, foliar nutrients were jointly influenced by functional dissimilarity, mycorrhizal type, and soil N availability. Among dissimilarity metrics, wood density (WD) dissimilarity was the strongest predictor. Specifically, functional dissimilarity consistently increased foliar N and P concentrations in AM trees across the soil total N level, whereas its effects on EcM trees shifted from positive to negative with increasing soil total N content. These diversity-driven increases in foliar P concentration were further associated with enhanced tree growth. Our findings demonstrate that mycorrhizal type and soil N availability jointly mediate effects of neighborhood diversity on tree foliar nutrient status, with foliar P concentration playing a pivotal role in driving productivity responses to biodiversity in subtropical forests.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.3,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shinde Nikhil, Habeeb Shaik Mohideen, Raja Natesan Sella
{"title":"LncRAnalyzer: a robust workflow for long non-coding RNA discovery using RNA-Seq","authors":"Shinde Nikhil, Habeeb Shaik Mohideen, Raja Natesan Sella","doi":"10.1111/tpj.70509","DOIUrl":"10.1111/tpj.70509","url":null,"abstract":"<div>\u0000 \u0000 <p>Long non-coding RNA (lncRNA) is a major transcript category that lacks protein-coding capabilities, with relatively low abundance and complex expression patterns. Distinguishing lncRNAs from protein-coding genes is a complex process involving multiple filtering steps. We developed an automated pipeline named LncRAnalyzer featuring retrained models for 60 species. This workflow aims to reduce the likelihood of obtaining protein-coding or partial protein-coding transcripts during lncRNA identification by utilizing eight distinct approaches. We conducted a 10-fold cross-validation of the sorghum models and training sets with their standard ones and other approaches using real-life RNA-Seq datasets and known lncRNA and CDS sequences of sorghum. The results showed that the sorghum models and training sets were outperformed. The pipeline output comprises upset plots illustrating the number of lncRNA/NPCTs identified by the approaches, commonly identified lncRNA and their classes, NPCTs, and expression count tables. A feature-level comparison and benchmarking analysis of LncRAnalyzer with four existing pipelines, namely, LncPipe, LncEvo, lncRNA-Annotation, and Plant-LncPipe, demonstrated that LncRAnalyzer is more comprehensive, easier to implement, and accurate in lncRNA predictions. This workflow also ascertains lncRNA origins from various Transposable Elements (TEs) in plants using TE annotations from APTEdb [http://apte.cp.utfpr.edu.br/]. LncRAnalyzer is publicly available on GitLab [https://gitlab.com/nikhilshinde0909/LncRAnalyzer.git] for academic users.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frank Wien, Nykola C Jones, Søren Vrønning Hoffmann, Véronique Arluison
{"title":"DNA methylation enhances cooperative disentanglement by the Hfq nucleoid-associated protein.","authors":"Frank Wien, Nykola C Jones, Søren Vrønning Hoffmann, Véronique Arluison","doi":"10.1007/s00249-025-01800-9","DOIUrl":"https://doi.org/10.1007/s00249-025-01800-9","url":null,"abstract":"<p><p>The Hfq protein is not only a mediator of RNA metabolism but also a key structural element involved in nucleic acid shaping. Its ability to compact and organize DNA, as well as its influence on the dynamics of various DNA-related processes, makes Hfq a central player in the regulation of bacterial chromosomal architecture and function. We previously demonstrated that different DNA methylation states affect Hfq binding and mobility. In this study, we show that Hfq, through its C-terminal region, can influence a DNA entangled/disentangled transition and examine the impact of DNA methylation on this previously uncharacterized function of Hfq. This discovery provides new insights into the role of Hfq in DNA transactions, with potential implications for essential cellular processes such as recombination and replication. Furthermore, this study demonstrates that Synchrotron Radiation Linear Dichroism (SRLD) is a powerful tool that can follow cooperative vs non-cooperative protein induced DNA structural transitions.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145298017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"miR159b, an epigenetic target of RSI1/FLD, negatively regulates systemic acquired resistance","authors":"Ranjan Kumar, Reena Saini, Deepjyoti Singh, Sujata Kaushik, Ashis Kumar Nandi","doi":"10.1111/tpj.70519","DOIUrl":"10.1111/tpj.70519","url":null,"abstract":"<div>\u0000 \u0000 <p>Plants retain memories of past infections to mount a robust defense in the form of systemic acquired resistance (SAR) during subsequent pathogen invasions. Primary infected tissues generate a group of compounds that serve as mobile signals for SAR development. Downstream processes subsequent to mobile signal perception are little known. Epigenetic regulator <i>reduced systemic immunity1/FLOWERING LOCUS D</i> (RSI1/FLD) is essential for activating SAR and functions downstream of signal perception in the systemic tissues. Here, we show that RSI1 negatively regulates the expression of miR159b, which in turn regulates the expression of a set of genes that control SAR development. RSI1 physically associates and contributes to SAR-associated demethylation of H3K4me2 and H3K4me3 at the <i>MIR159B</i> locus. Overexpression of miR159b suppresses SAR development, whereas SAR is exaggerated in <i>mir159ab</i> double mutants and target mimic expressing STTM159 lines. Through bioinformatics and expression analysis, we identified several targets of miR159, among which <i>SDG14</i>, <i>RD19A</i>, <i>MYB65</i>, <i>MYB33</i>, <i>MYB120</i>, <i>TPST</i>, <i>TIE4</i>, <i>CSD3</i>, and <i>PPDK</i> positively regulate SAR development, whereas <i>MYB97</i> and <i>MYB104</i> negatively regulate it. Altogether, our work identified a functional network of genes that activate and fine-tune SAR development in <i>Arabidopsis thaliana</i>.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fang He, Peng Yang, Yuan Zhang, Hao Li, Shu-Ying Wei, Shuang-Lian Deng, Jia-hui Liu, Ting Wang, Bo Li, Tiantian Lin
{"title":"The PtrRZFP4-PtrJAZ2 module regulates the jasmonic acid signaling pathway involved in the interaction between poplar and herbivorous insects","authors":"Fang He, Peng Yang, Yuan Zhang, Hao Li, Shu-Ying Wei, Shuang-Lian Deng, Jia-hui Liu, Ting Wang, Bo Li, Tiantian Lin","doi":"10.1111/tpj.70502","DOIUrl":"10.1111/tpj.70502","url":null,"abstract":"<div>\u0000 \u0000 <p>The plant hormone jasmonic acid (JA) is pivotal in regulating plant growth and defense mechanisms. Despite extensive research on the JA signaling network, the integration of other factors with JAZ (jasmonate ZIM domain) proteins to modulate JA signaling in response to diverse herbivore attacks remains unclear. In this study, we employed molecular biology and multi-omics techniques to identify an E3 ubiquitin ligase, PtrRZFP4. This E3 ubiquitin ligase exerts a positive regulatory effect on the JA signaling pathway, yet demonstrates differential responses to distinct insect types. We found that upon insect attack, the expression of <i>PtrRZFP4</i> transcripts is upregulated. In addition, PtrRZFP4 is able to interact with PtrJAZ2 and promote the ubiquitination and degradation of PtrJAZ2 protein. Furthermore, <i>PtrRZFP4</i> activates the jasmonic acid (JA) signaling pathway at both the transcriptional and metabolic levels, triggering the synthesis of a large number of secondary metabolites related to insect resistance, such as terpenoids and alkaloids. This ultimately enhances the plant's defense against insect herbivory. The larvae of the specialist insect showed a strong preference for feeding on the leaves of transgenic poplar overexpressing <i>PtrRZFP4</i> (<i>OX-PtrRZFP4</i>), which contain elevated levels of secondary metabolites. In contrast, the larvae of the generalist insect avoid leaves with increased secondary metabolite levels. However, <i>PtrJAZ2</i> exhibits an opposite function to <i>PtrRZFP4</i> in the resistance of poplar trees to different herbivores. Therefore, our study uncovers the significant role of the PtrRZFP4-PtrJAZ2 module in plant JA signaling and resistance to insect herbivory, highlighting its potential for biotechnological applications in improving herbivore resistance in forest trees.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Turbo-charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond","authors":"Kangquan Yin, Chung-Jui Tsai","doi":"10.1111/tpj.70527","DOIUrl":"10.1111/tpj.70527","url":null,"abstract":"<p>Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and <i>de novo</i> domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene-free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High-throughput sequencing technologies, including long-read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user-friendly, synthetic biology-compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue-specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next-generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"124 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12527382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}