Amaranthus palmeri is one of the most troublesome invasive agricultural weeds worldwide, exhibiting super invasiveness and high resistance to conventional management strategies. Artificial microRNA-mediated silencing technology, coupled with a nanoparticle-mediated delivery system, represents an attractive approach for fertility control in A. palmeri. In this study, we first characterised the biological function of ApMIR319 via ectopic overexpression in Arabidopsis, identifying it as a crucial candidate molecular target for fertility regulation in A. palmeri. Subsequently, we prepared layered double hydroxide (LDH) nanosheets using the co-precipitation-hydrothermal method. Employing the LDH nanosheets as nanocarriers, we implemented nearly complete encapsulation of the ApmiR319 mimic at a mass ratio of 1:100. The LDH-ApmiR319 mimic complex exhibited stable loading capacity in neutral and alkaline solutions. Furthermore, the LDH-ApmiR319 mimic complex demonstrated robust adhesion to leaf surfaces and enhanced resistance to enzymatic degradation. Spraying treatments with the LDH-ApmiR319 mimic complex significantly elevated ApmiR319 expression levels in male florets, while concurrently down-regulating its target genes (ApTCP4, ApTCP10 and ApMYB33), thereby inhibiting pollen development in A. palmeri. In conclusion, this study successfully established an LDH nanosheet-mediated delivery system of ApmiR319 mimic for male fertility control in A. palmeri. It represents a novel strategy and direction for achieving sustainable management of this weed.
{"title":"Molecular Targeted Suppression of Male Fertility in Amaranthus palmeri S. Watson: Function and Layered Double Hydroxide Nanosheets-Based Delivery System of ApmiR319.","authors":"Liyong Sun,Yusen Wang,Minglu Yin,Lina Xu,Yao Chen,Shuxian Li,Zengfang Yin","doi":"10.1111/pbi.70564","DOIUrl":"https://doi.org/10.1111/pbi.70564","url":null,"abstract":"Amaranthus palmeri is one of the most troublesome invasive agricultural weeds worldwide, exhibiting super invasiveness and high resistance to conventional management strategies. Artificial microRNA-mediated silencing technology, coupled with a nanoparticle-mediated delivery system, represents an attractive approach for fertility control in A. palmeri. In this study, we first characterised the biological function of ApMIR319 via ectopic overexpression in Arabidopsis, identifying it as a crucial candidate molecular target for fertility regulation in A. palmeri. Subsequently, we prepared layered double hydroxide (LDH) nanosheets using the co-precipitation-hydrothermal method. Employing the LDH nanosheets as nanocarriers, we implemented nearly complete encapsulation of the ApmiR319 mimic at a mass ratio of 1:100. The LDH-ApmiR319 mimic complex exhibited stable loading capacity in neutral and alkaline solutions. Furthermore, the LDH-ApmiR319 mimic complex demonstrated robust adhesion to leaf surfaces and enhanced resistance to enzymatic degradation. Spraying treatments with the LDH-ApmiR319 mimic complex significantly elevated ApmiR319 expression levels in male florets, while concurrently down-regulating its target genes (ApTCP4, ApTCP10 and ApMYB33), thereby inhibiting pollen development in A. palmeri. In conclusion, this study successfully established an LDH nanosheet-mediated delivery system of ApmiR319 mimic for male fertility control in A. palmeri. It represents a novel strategy and direction for achieving sustainable management of this weed.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"83 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073097","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}
7-β-xylosyl-10-deacetyltaxol (XDT) is much more abundant than the anticancer drug Taxol in Taxus species and is usually regarded as the by-product of Taxol. It could be enzymatically transformed into 10-deacetyltaxol (DT), and the latter could be further converted into Taxol. The enzyme 10-deacetylbaccatin III-10-β-O-acetyltransferase (DBAT) can acetylate the non-natural substrate DT into Taxol, but the conversion efficiency was extremely low. Herein, we globally redesigned DBATcus from Taxus cuspidata to improve its efficiency in DT acetylation through combinatorial protein engineering strategies including virtual saturation mutagenesis, in silico screening, DNA shuffling, and iterative combinatorial mutagenesis. Several more active DBAT mutants against DT were obtained, among which the ICM9-6 exhibited 16.4 times higher activity than DBATcus. The transient expression system of Nicotiana benthamiana was then established, and the ICM9-6 was functionally expressed in the system, with yield of 8.2 μg g-1 FW (129.3 μg g-1 DW) Taxol when the system was fed with DT. Specifically, the fungal glycoside hydrolase LXYL-P1-2 that was responsible for converting XDT into DT was also functionally expressed in the system, and upon feeding XDT, the co-expression of LXYL-P1-2 and ICM9-6 yielded 3.6 μg g-1 FW (55.4 μg g-1 DW) Taxol. These results represent the highest reported Taxol productivity in the tobacco system to date and lay a foundation for the construction of the stable transgenic cell lines of tobacco and more efficiently converting DT or XDT into Taxol for the large-scale pharmaceutical manufacturing.
{"title":"Engineering of 10-Deacetylbaccatin III-10-β-O-Acetyltransferase From Taxus Species for Efficient Acetylating Non-Natural Substrates Into Taxol in Nicotiana benthamiana.","authors":"Tian-Jiao Chen,Jing-Jing Chen,Xiao-Yan Sun,Ting Gong,Jin-Ling Yang,Ping Zhu","doi":"10.1111/pbi.70566","DOIUrl":"https://doi.org/10.1111/pbi.70566","url":null,"abstract":"7-β-xylosyl-10-deacetyltaxol (XDT) is much more abundant than the anticancer drug Taxol in Taxus species and is usually regarded as the by-product of Taxol. It could be enzymatically transformed into 10-deacetyltaxol (DT), and the latter could be further converted into Taxol. The enzyme 10-deacetylbaccatin III-10-β-O-acetyltransferase (DBAT) can acetylate the non-natural substrate DT into Taxol, but the conversion efficiency was extremely low. Herein, we globally redesigned DBATcus from Taxus cuspidata to improve its efficiency in DT acetylation through combinatorial protein engineering strategies including virtual saturation mutagenesis, in silico screening, DNA shuffling, and iterative combinatorial mutagenesis. Several more active DBAT mutants against DT were obtained, among which the ICM9-6 exhibited 16.4 times higher activity than DBATcus. The transient expression system of Nicotiana benthamiana was then established, and the ICM9-6 was functionally expressed in the system, with yield of 8.2 μg g-1 FW (129.3 μg g-1 DW) Taxol when the system was fed with DT. Specifically, the fungal glycoside hydrolase LXYL-P1-2 that was responsible for converting XDT into DT was also functionally expressed in the system, and upon feeding XDT, the co-expression of LXYL-P1-2 and ICM9-6 yielded 3.6 μg g-1 FW (55.4 μg g-1 DW) Taxol. These results represent the highest reported Taxol productivity in the tobacco system to date and lay a foundation for the construction of the stable transgenic cell lines of tobacco and more efficiently converting DT or XDT into Taxol for the large-scale pharmaceutical manufacturing.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"1 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088941","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}
Kelly L. Vomo‐Donfack, Mariem Abaach, Ana M. Luna, Grégory Ginot, Verónica G. Doblas, Ian Morilla
Small signalling peptides (SSPs) serve as crucial mediators of cell‐to‐cell communication in plants, orchestrating diverse physiological processes from development to stress responses. While recent advances in sequencing technologies have improved genome annotation, the identification of novel SSPs remains challenging due to their small size, sequence diversity, and often transient expression patterns. To address this bottleneck, we developed S 2 ‐PepAnalyst, a machine learning‐powered web tool that integrates plant‐specific datasets with advanced computational approaches for SSP prediction and classification. Our platform combines protein language models with geometric‐topological feature analysis to capture both sequence and structural characteristics of known SSP families. When validated against experimentally confirmed peptides, S 2 ‐PepAnalyst achieved high predictive accuracy (99.5%) while maintaining low false‐negative rates. The tool successfully classified peptides into functionally distinct families (e.g., CLE, RALF) and identified non‐canonical SSPs that lack traditional signal peptides. Importantly, S 2 ‐PepAnalyst demonstrated robust performance across both model plants and agriculturally important species. As a freely available resource ( https://www.s2‐pepanalyst.uma.es ), this tool will empower plant biologists to systematically explore the largely untapped repertoire of plant SSPs, facilitating discoveries in plant cell signalling and potential applications in crop improvement.
{"title":" S 2 ‐ PepAnalyst : A Web Tool for Predicting Plant Small Signalling Peptides","authors":"Kelly L. Vomo‐Donfack, Mariem Abaach, Ana M. Luna, Grégory Ginot, Verónica G. Doblas, Ian Morilla","doi":"10.1111/pbi.70536","DOIUrl":"https://doi.org/10.1111/pbi.70536","url":null,"abstract":"Small signalling peptides (SSPs) serve as crucial mediators of cell‐to‐cell communication in plants, orchestrating diverse physiological processes from development to stress responses. While recent advances in sequencing technologies have improved genome annotation, the identification of novel SSPs remains challenging due to their small size, sequence diversity, and often transient expression patterns. To address this bottleneck, we developed S <jats:sup>2</jats:sup> ‐PepAnalyst, a machine learning‐powered web tool that integrates plant‐specific datasets with advanced computational approaches for SSP prediction and classification. Our platform combines protein language models with geometric‐topological feature analysis to capture both sequence and structural characteristics of known SSP families. When validated against experimentally confirmed peptides, S <jats:sup>2</jats:sup> ‐PepAnalyst achieved high predictive accuracy (99.5%) while maintaining low false‐negative rates. The tool successfully classified peptides into functionally distinct families (e.g., CLE, RALF) and identified non‐canonical SSPs that lack traditional signal peptides. Importantly, S <jats:sup>2</jats:sup> ‐PepAnalyst demonstrated robust performance across both model plants and agriculturally important species. As a freely available resource ( <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://www.s2-pepanalyst.uma.es\">https://www.s2‐pepanalyst.uma.es</jats:ext-link> ), this tool will empower plant biologists to systematically explore the largely untapped repertoire of plant SSPs, facilitating discoveries in plant cell signalling and potential applications in crop improvement.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"86 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071706","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":"High-Quality Chromosome-Level Genomes Reveal the Structure and Evolution of the S and Z Self-Incompatibility Loci in Leymus Chinensis.","authors":"Sijie Sun,Jianli Wang,Yu Guan,Hongkui Zhang,Linlin Mu,Xu Zhuang,Dongmei Zhang,Sizhong Li,Mengjie Zhao,Zhelong Lin,Shuaibin Zhang,Xiaofeng Cao,Youfa Cheng,Zhongbao Shen,Yu'e Zhang,Yongbiao Xue","doi":"10.1111/pbi.70565","DOIUrl":"https://doi.org/10.1111/pbi.70565","url":null,"abstract":"","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"2020 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073161","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}
Yike Su, Xiaojuan Yang, Chanyuan Wu, Xianyao Jin, Yuanyuan Zhang, Yuyan Zhang, Kunsong Chen, Mingliang Yu, Bo Zhang
Free amino acids (FAAs) play a fundamental role in determining fruit quality and stress adaptation, yet their genetic regulation remains poorly understood. Through an integrated approach combining metabolomic and sensory analyses of 120 peach ( Prunus persica ) hybrids, we identified glutamate as a key metabolite linking FAA content to umami taste perception. By combining genome‐wide association studies (GWAS) with expression quantitative trait locus (eQTL) mapping, we identified PpGGAT1 (glutamate:glyoxylate aminotransferase) and the zinc finger transcription factor PpC2H2‐3 as central regulators of glutamate metabolism. Functional characterisation revealed that overexpression of PpGGAT1 led to reduced glutamate levels and diminished umami intensity, whereas PpC2H2‐3 transcriptionally suppresses PpGGAT1 to enhance glutamate accumulation. Notably, elevated glutamate levels enhanced resistance to Monilinia fructicola infection, with both genes showing significant expression changes during the progression of brown rot disease. Comparative analysis further indicated that freestone cultivars exhibit superior glutamate accumulation, a trait confirmed across 100 commercial varieties. Our findings reveal a novel regulatory module, PpC2H2‐3‐PpGGAT1, that coordinately modulates fruit flavour quality and defence responses against pathogens. This study provides mechanistic insights into FAA regulation in fruit crops and identifies actionable molecular targets for the development of varieties with enhanced sensory attributes and disease resistance.
{"title":"The C2H2 ‐ GGAT Regulatory Module Fine‐Tunes Glutamate Homeostasis to Improve Fruit Flavour and Enhance Disease Resistance in Peach","authors":"Yike Su, Xiaojuan Yang, Chanyuan Wu, Xianyao Jin, Yuanyuan Zhang, Yuyan Zhang, Kunsong Chen, Mingliang Yu, Bo Zhang","doi":"10.1111/pbi.70569","DOIUrl":"https://doi.org/10.1111/pbi.70569","url":null,"abstract":"Free amino acids (FAAs) play a fundamental role in determining fruit quality and stress adaptation, yet their genetic regulation remains poorly understood. Through an integrated approach combining metabolomic and sensory analyses of 120 peach ( <jats:styled-content style=\"fixed-case\"> <jats:italic>Prunus persica</jats:italic> </jats:styled-content> ) hybrids, we identified glutamate as a key metabolite linking FAA content to umami taste perception. By combining genome‐wide association studies (GWAS) with expression quantitative trait locus (eQTL) mapping, we identified <jats:italic>PpGGAT1</jats:italic> (glutamate:glyoxylate aminotransferase) and the zinc finger transcription factor PpC2H2‐3 as central regulators of glutamate metabolism. Functional characterisation revealed that overexpression of <jats:italic>PpGGAT1</jats:italic> led to reduced glutamate levels and diminished umami intensity, whereas PpC2H2‐3 transcriptionally suppresses <jats:italic>PpGGAT1</jats:italic> to enhance glutamate accumulation. Notably, elevated glutamate levels enhanced resistance to <jats:styled-content style=\"fixed-case\"> <jats:italic>Monilinia fructicola</jats:italic> </jats:styled-content> infection, with both genes showing significant expression changes during the progression of brown rot disease. Comparative analysis further indicated that freestone cultivars exhibit superior glutamate accumulation, a trait confirmed across 100 commercial varieties. Our findings reveal a novel regulatory module, PpC2H2‐3‐PpGGAT1, that coordinately modulates fruit flavour quality and defence responses against pathogens. This study provides mechanistic insights into FAA regulation in fruit crops and identifies actionable molecular targets for the development of varieties with enhanced sensory attributes and disease resistance.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"58 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071610","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}
Morgan W. Kirzinger, Sarika Saini, Andrea T. Todd, Ushan Alahakoon, Kevin C. Koh, Justin B. Nichol, HaiYing Yuan, Kevin Fengler, Victor Llaca, Dustin Cram, Sampath Perumal, Wali Soomro, Magda Konopka, Tancey Melchkart, Venkat Bandi, Yasmina Bekkaoui, Yifang Tan, Chad Matsalla, Andrew G. Sharpe, Carl Gutwin, Fred Thoonen, Igor Falak, Chad Koscielny, Stuart Gardner, Isobel A. P. Parkin, Marcus A. Samuel, Alison M. R. Ferrie, Dave Charne, Daoquan Xiang, Jetty S. S. AmmiRaju, Sateesh Kagale
A key challenge for the genetic improvement of canola ( Brassica napus ), one of the world's most important oilseeds, is the limited natural variation for commercially important traits. The creation of new variation is hindered by the lack of functional knowledge about genes controlling these traits. Ploidy and genomic duplications in canola complicate the effective transfer of functional insights from Arabidopsis. Here, we report a novel functional genomics platform for rapid gene/trait discovery and optimisation. We established a double haploid population of 1240 lines from EMS‐mutagenised microspores of the spring‐type canola line, NRCDH4079. A platinum‐quality reference genome, gene annotations and a gene expression atlas from developing seeds were generated for NRCDH4079. Exome sequencing of the mutagenised population resulted in the development of a ‘TILLED’ database, revealing 1243 premature stop codons across 1222 genes, along with 140 522 moderate‐effect or modifier variants impacting 70 626 genes. Phenotypic analysis revealed significant variation in key seed traits, including oil, protein and acid detergent fibre (ADF). Notably, the mutant variant DP125410314 exhibited increased protein and reduced ADF, two important traits for improving the meal composition of canola. Genetic mapping of this variant identified a homoeologous non‐reciprocal translocation between A1 and C1 chromosomes associated with reduced ADF content, highlighting the role of structural variations in trait development. This work establishes haploid mutagenesis as a powerful tool for crop improvement, with broader implications for other Brassica species. By enhancing our understanding of seed protein traits, it lays the foundation for canola varieties that meet future nutritional and market demands.
{"title":"Haploid Mutation Mapping Identifies a Homoeologous Non‐Reciprocal Translocation Linked to Reduced Fibre and Enhanced Protein in Brassica napus ","authors":"Morgan W. Kirzinger, Sarika Saini, Andrea T. Todd, Ushan Alahakoon, Kevin C. Koh, Justin B. Nichol, HaiYing Yuan, Kevin Fengler, Victor Llaca, Dustin Cram, Sampath Perumal, Wali Soomro, Magda Konopka, Tancey Melchkart, Venkat Bandi, Yasmina Bekkaoui, Yifang Tan, Chad Matsalla, Andrew G. Sharpe, Carl Gutwin, Fred Thoonen, Igor Falak, Chad Koscielny, Stuart Gardner, Isobel A. P. Parkin, Marcus A. Samuel, Alison M. R. Ferrie, Dave Charne, Daoquan Xiang, Jetty S. S. AmmiRaju, Sateesh Kagale","doi":"10.1111/pbi.70535","DOIUrl":"https://doi.org/10.1111/pbi.70535","url":null,"abstract":"A key challenge for the genetic improvement of canola ( <jats:styled-content style=\"fixed-case\"> <jats:italic>Brassica napus</jats:italic> </jats:styled-content> ), one of the world's most important oilseeds, is the limited natural variation for commercially important traits. The creation of new variation is hindered by the lack of functional knowledge about genes controlling these traits. Ploidy and genomic duplications in canola complicate the effective transfer of functional insights from Arabidopsis. Here, we report a novel functional genomics platform for rapid gene/trait discovery and optimisation. We established a double haploid population of 1240 lines from EMS‐mutagenised microspores of the spring‐type canola line, NRCDH4079. A platinum‐quality reference genome, gene annotations and a gene expression atlas from developing seeds were generated for NRCDH4079. Exome sequencing of the mutagenised population resulted in the development of a ‘TILLED’ database, revealing 1243 premature stop codons across 1222 genes, along with 140 522 moderate‐effect or modifier variants impacting 70 626 genes. Phenotypic analysis revealed significant variation in key seed traits, including oil, protein and acid detergent fibre (ADF). Notably, the mutant variant DP125410314 exhibited increased protein and reduced ADF, two important traits for improving the meal composition of canola. Genetic mapping of this variant identified a homoeologous non‐reciprocal translocation between A1 and C1 chromosomes associated with reduced ADF content, highlighting the role of structural variations in trait development. This work establishes haploid mutagenesis as a powerful tool for crop improvement, with broader implications for other <jats:italic>Brassica</jats:italic> species. By enhancing our understanding of seed protein traits, it lays the foundation for canola varieties that meet future nutritional and market demands.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"297 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071671","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}
Zuba Ahmed, Jiyuan An, Satomi Hayashi, Julia Bally, Chris Winefield, Peter M. Waterhouse
Forward genetics has been instrumental in identifying genes underlying desirable traits, yet its application to polyploid plants, many of which are key agricultural crops, remains challenging due to their genomic complexity. Therefore, we developed BenthMap, a bulk segregant analysis platform for high‐throughput trait mapping and gene discovery, in the allotetraploid model plant Nicotiana benthamiana . BenthMap leverages high‐quality genome assemblies of two genetically and phenotypically distinct strains, LAB and QLD. To validate the pipeline, we investigated their contrasting anthocyanin responses. Transient overexpression of AcMYB110 , an activation regulator of anthocyanin biosynthesis, induces robust anthocyanin production in QLD leaves but gives a detrimental, often necrotic, response in LAB. Using BenthMap and a population derived from selfing the F1 hybrid of a LAB × QLD cross (F1S1 population), with genome coverage as low as 10×, we mapped the necrotic LAB response to a 3.5 Mb homozygous region on chromosome 10. This region contains a leucoanthocyanidin dioxygenase gene. Transiently expressing the QLD version of this gene, along with AcMYB110 , restored robust anthocyanin accumulation in LAB, validating the causal gene. These findings demonstrate BenthMap's utility for rapid trait‐gene identification in N. benthamiana and have potential for application to other allopolyploid plants.
{"title":"Harnessing Bulk‐Segregant Mapping to Identify Trait‐Associated Genes in the Allopolyploid Model Plant Nicotiana benthamiana","authors":"Zuba Ahmed, Jiyuan An, Satomi Hayashi, Julia Bally, Chris Winefield, Peter M. Waterhouse","doi":"10.1111/pbi.70560","DOIUrl":"https://doi.org/10.1111/pbi.70560","url":null,"abstract":"Forward genetics has been instrumental in identifying genes underlying desirable traits, yet its application to polyploid plants, many of which are key agricultural crops, remains challenging due to their genomic complexity. Therefore, we developed BenthMap, a bulk segregant analysis platform for high‐throughput trait mapping and gene discovery, in the allotetraploid model plant <jats:italic>Nicotiana benthamiana</jats:italic> . BenthMap leverages high‐quality genome assemblies of two genetically and phenotypically distinct strains, LAB and QLD. To validate the pipeline, we investigated their contrasting anthocyanin responses. Transient overexpression of <jats:italic>AcMYB110</jats:italic> , an activation regulator of anthocyanin biosynthesis, induces robust anthocyanin production in QLD leaves but gives a detrimental, often necrotic, response in LAB. Using BenthMap and a population derived from selfing the F1 hybrid of a LAB × QLD cross (F1S1 population), with genome coverage as low as 10×, we mapped the necrotic LAB response to a 3.5 Mb homozygous region on chromosome 10. This region contains a leucoanthocyanidin dioxygenase gene. Transiently expressing the QLD version of this gene, along with <jats:italic>AcMYB110</jats:italic> , restored robust anthocyanin accumulation in LAB, validating the causal gene. These findings demonstrate BenthMap's utility for rapid trait‐gene identification in <jats:italic>N. benthamiana</jats:italic> and have potential for application to other allopolyploid plants.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"7 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071607","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}
Introduction of Reduced height ( Rht ) genes into modern wheat cultivars has resulted in ‘Green Revolution’ that skyrocketed wheat grain yields worldwide since the 1960s. These ‘Green Revolution’ cultivars show shorter plant height, but higher lodging resistance and harvest index. The identification and exploitation of novel Rht genes are of great significance for the development of high‐yielding wheat cultivars. In this study, a semi‐dwarf wheat mutant, d14078 , with reduced plant height and grain size, was generated by ethyl methanesulfonate (EMS) mutagenesis. Here, through map‐based cloning, we cloned the causal gene for the semi‐dwarf phenotype of d14078 as TaWAK3‐B that encodes a cell wall‐associated receptor kinase 3. A single‐base mutation occurred in the coding region of TaWAK3‐B , resulting in an amino acid mutation from Glu to Lys (E938K) at residue 938, which reduces its stability and the formation of homodimers. The cytoskeletons were changed in both the d14078 and TaWAK3‐B knockout mutants, as well as the TaWAK3‐B overexpression of transgenic plants. Further investigation revealed that TaWAK3‐B directly forms stable protein assembly with TaADF3‐A (actin depolymerisation factor), TaKLCR1‐A (kinesin light chain‐related protein 1), and TaIQD2‐D (IQ67‐domain protein 2). These interactions and complex formations were significantly attenuated by the TaWAK3‐B E938K mutation. Therefore, our findings clarify TaWAK3‐B regulating the microfilament and microtubule formation that elucidate on the regulation of wheat stem development.
{"title":"A Single‐Base Mutation in TaWAK3‐B Reduces Plant Height via Cytoskeleton in Bread Wheat","authors":"Naijiao Wang, Ruolin Bian, Dejie Du, Yunjie Liu, Yiao Ma, Zihao Jiang, Zhaoju Li, Yan Zhou, Xiangyu Zhang, Zhaoheng Zhang, Beilu Cao, Xiongtao Li, Zhaoyan Chen, Jie Liu, Qixin Sun, Zhongfu Ni, Lingling Chai","doi":"10.1111/pbi.70563","DOIUrl":"https://doi.org/10.1111/pbi.70563","url":null,"abstract":"Introduction of <jats:italic>Reduced height</jats:italic> ( <jats:italic>Rht</jats:italic> ) genes into modern wheat cultivars has resulted in ‘Green Revolution’ that skyrocketed wheat grain yields worldwide since the 1960s. These ‘Green Revolution’ cultivars show shorter plant height, but higher lodging resistance and harvest index. The identification and exploitation of novel <jats:italic>Rht</jats:italic> genes are of great significance for the development of high‐yielding wheat cultivars. In this study, a semi‐dwarf wheat mutant, <jats:italic>d14078</jats:italic> , with reduced plant height and grain size, was generated by ethyl methanesulfonate (EMS) mutagenesis. Here, through map‐based cloning, we cloned the causal gene for the semi‐dwarf phenotype of <jats:italic>d14078</jats:italic> as <jats:italic>TaWAK3‐B</jats:italic> that encodes a cell wall‐associated receptor kinase 3. A single‐base mutation occurred in the coding region of <jats:italic>TaWAK3‐B</jats:italic> , resulting in an amino acid mutation from Glu to Lys (E938K) at residue 938, which reduces its stability and the formation of homodimers. The cytoskeletons were changed in both the <jats:italic>d14078</jats:italic> and <jats:italic>TaWAK3‐B</jats:italic> knockout mutants, as well as the <jats:italic>TaWAK3‐B</jats:italic> overexpression of transgenic plants. Further investigation revealed that TaWAK3‐B directly forms stable protein assembly with TaADF3‐A (actin depolymerisation factor), TaKLCR1‐A (kinesin light chain‐related protein 1), and TaIQD2‐D (IQ67‐domain protein 2). These interactions and complex formations were significantly attenuated by the TaWAK3‐B <jats:sup>E938K</jats:sup> mutation. Therefore, our findings clarify <jats:italic>TaWAK3‐B</jats:italic> regulating the microfilament and microtubule formation that elucidate on the regulation of wheat stem development.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"143 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071705","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}
Kangting Dong, Chang Liu, Mingyue Wang, Dayong Li, Jialin Li, Ning Zhao, Jianmiao Sun, Xiaodong Wang, Hongjie Di, Hong Luo, Xinbo Sun
MicroRNA319 (miR319) has been demonstrated to regulate plant development and responses to stress such as drought and salt. However, its role in thermotolerance, particularly in cool season grasses, remains unclear. Here we report that miR319 plays a negative role in heat tolerance of creeping bentgrass ( Agrostis stolonifera ). A basic helix–loop–helix (bHLH) transcription factor, AsbHLH094 was identified as the target gene of miR319, and its expression was significantly downregulated in the miR319‐overexpressing (OE319) transgenic creeping bentgrass lines. Functional characterisation revealed that overexpression of AsbHLH094 enhanced heat tolerance of the transgenic tobacco plants. Furthermore, protein–protein interaction assays confirmed that AsbHLH094 physically interacts with AsIAA1, an Aux/IAA protein involved in auxin signalling. Transcriptomic analysis showed that auxin biosynthesis genes such as TARs , YUCCAs , along with auxin‐response genes including Auxin/IAAs and ARFs were downregulated in the OE319 transgenic creeping bentgrass plants, leading to reduced auxin accumulation, while elevated auxin levels and induced changes in auxin biosynthesis‐ and response‐related genes were observed in the AsbHLH094 overexpression tobacco. Endogenous indole‐3‐acetic acid (IAA) levels in creeping bentgrass were significantly increased under high‐temperature conditions, and exogenous application of IAA at appropriate concentrations improved heat tolerance in creeping bentgrass. Together, our findings reveal a previously uncharacterized miR319‐AsbHLH094 regulatory module that modulates auxin biosynthesis and signalling, thereby contributing to heat stress responses in creeping bentgrass.
{"title":"The miR319 / bHLH094 Module Regulates Creeping Bentgrass Thermotolerance by Modulating Auxin Biosynthesis and Signalling Pathway","authors":"Kangting Dong, Chang Liu, Mingyue Wang, Dayong Li, Jialin Li, Ning Zhao, Jianmiao Sun, Xiaodong Wang, Hongjie Di, Hong Luo, Xinbo Sun","doi":"10.1111/pbi.70545","DOIUrl":"https://doi.org/10.1111/pbi.70545","url":null,"abstract":"MicroRNA319 (miR319) has been demonstrated to regulate plant development and responses to stress such as drought and salt. However, its role in thermotolerance, particularly in cool season grasses, remains unclear. Here we report that miR319 plays a negative role in heat tolerance of creeping bentgrass ( <jats:styled-content style=\"fixed-case\"> <jats:italic>Agrostis stolonifera</jats:italic> </jats:styled-content> ). A basic helix–loop–helix (bHLH) transcription factor, AsbHLH094 was identified as the target gene of miR319, and its expression was significantly downregulated in the miR319‐overexpressing (OE319) transgenic creeping bentgrass lines. Functional characterisation revealed that overexpression of AsbHLH094 enhanced heat tolerance of the transgenic tobacco plants. Furthermore, protein–protein interaction assays confirmed that AsbHLH094 physically interacts with AsIAA1, an Aux/IAA protein involved in auxin signalling. Transcriptomic analysis showed that auxin biosynthesis genes such as <jats:italic>TARs</jats:italic> , <jats:italic>YUCCAs</jats:italic> , along with auxin‐response genes including <jats:italic>Auxin/IAAs</jats:italic> and <jats:italic>ARFs</jats:italic> were downregulated in the OE319 transgenic creeping bentgrass plants, leading to reduced auxin accumulation, while elevated auxin levels and induced changes in auxin biosynthesis‐ and response‐related genes were observed in the AsbHLH094 overexpression tobacco. Endogenous indole‐3‐acetic acid (IAA) levels in creeping bentgrass were significantly increased under high‐temperature conditions, and exogenous application of IAA at appropriate concentrations improved heat tolerance in creeping bentgrass. Together, our findings reveal a previously uncharacterized miR319‐AsbHLH094 regulatory module that modulates auxin biosynthesis and signalling, thereby contributing to heat stress responses in creeping bentgrass.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"73 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056277","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}
Floral ultraviolet (UV) patterns are visible to bee pollinators and can affect crop yields by impacting pollinator visitation. However, the mechanisms underlying the intraspecific variations of UV bullseye size remain largely unknown. We analyse the ecological consequences and genetic basis of floral UV bullseye size variation in an important oil crop at high altitudes, Brassica rapa subsp. oleifera (turnip rape). Flowers with larger UV bullseye attract more bees and produce more seeds. The transcription factor BrobZIP16 was newly identified as a key determinant of large UV bullseye, supported by evidence of its high expression and selective sweeps in plants with larger UV bullseye. BrobZIP16 regulates UV bullseye size by interacting with the known regulator BroMYB111 in the flavonoid biosynthetic pathway and accumulating UV‐absorbing flavonols. Our results reveal the mechanisms underlying intraspecific UV bullseye size variations, and such ‘cryptic’ large bullseye can be targeted in molecular breeding to increase oilseed production.
{"title":"Genetic Basis of UV Bullseye Size Variations in Turnip Rape ( Brassica rapa subsp. oleifera )","authors":"Zhi‐Li Zhou, Yu Zhang, Li‐Ling Jiang, An‐Ning Li, Guo‐Peng Zhang, Ming‐Liu Yang, Zhi‐Qiang Zhang, Dong‐Rui Jia, Bin Tian, Xu‐Dong Sun, Yong‐Ping Yang, Yuan‐Wen Duan","doi":"10.1111/pbi.70540","DOIUrl":"https://doi.org/10.1111/pbi.70540","url":null,"abstract":"Floral ultraviolet (UV) patterns are visible to bee pollinators and can affect crop yields by impacting pollinator visitation. However, the mechanisms underlying the intraspecific variations of UV bullseye size remain largely unknown. We analyse the ecological consequences and genetic basis of floral UV bullseye size variation in an important oil crop at high altitudes, <jats:styled-content style=\"fixed-case\"> <jats:italic>Brassica rapa</jats:italic> </jats:styled-content> subsp. <jats:italic>oleifera</jats:italic> (turnip rape). Flowers with larger UV bullseye attract more bees and produce more seeds. The transcription factor BrobZIP16 was newly identified as a key determinant of large UV bullseye, supported by evidence of its high expression and selective sweeps in plants with larger UV bullseye. BrobZIP16 regulates UV bullseye size by interacting with the known regulator BroMYB111 in the flavonoid biosynthetic pathway and accumulating UV‐absorbing flavonols. Our results reveal the mechanisms underlying intraspecific UV bullseye size variations, and such ‘cryptic’ large bullseye can be targeted in molecular breeding to increase oilseed production.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"76 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047932","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}
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