Wenxue Wu, Congcong Jiang, Guangqi Gao, Namiki Mitani-Ueno, Yu Guo, Jinhong Kan, Yehui Xiong, Martin Mascher, Zhongfu Ni, Jian Feng Ma, Ke Wang, Ping Yang
{"title":"Spatial Regulation of Silicon Accumulation in Peduncle Confers Sheathed Spike in Barley","authors":"Wenxue Wu, Congcong Jiang, Guangqi Gao, Namiki Mitani-Ueno, Yu Guo, Jinhong Kan, Yehui Xiong, Martin Mascher, Zhongfu Ni, Jian Feng Ma, Ke Wang, Ping Yang","doi":"10.1111/pbi.70666","DOIUrl":"10.1111/pbi.70666","url":null,"abstract":"<p>Peduncle, the uppermost internode in cereals, connects the stem to the inflorescence and is critical for the transport of water, nutrients and photosynthetic assimilates. While peduncle length associates with plant height and its elongation is primarily regulated by phytohormones, we report a previously unrecognized mechanism involving the spatial distribution of silicon (Si). We identified a barley mutant, <i>sheathed spike 2</i> (<i>ss2</i>), characterized by a specifically shortened peduncle that traps the spike within the flag leaf sheath. Positional cloning and analysis of allelic mutants revealed that the wild-type <i>SS2</i> gene encodes a putative silicon efflux transporter. <i>SS2</i> is expressed throughout the lifecycle, with higher transcriptional levels in the rachis and stem internodes, and its encoded protein localizes to the plasma membrane. We demonstrate that SS2 is required for polarized Si partitioning. Unlike wild-type plants, which ultimately deposit Si in spikes, the <i>ss2</i> mutant exhibits an 8-fold increase in Si accumulation in the peduncle and a significant increase in the flag leaf. Hydroponic experiments without Si supply restored normal peduncle elongation in the <i>ss2</i> mutant, demonstrating that local Si hyper-accumulation directly inhibits elongation. The conserved role of <i>SS2</i> was supported by diversity analysis across barley and common wheat, as well as by the similar sheathed spike phenotype in tetraploid wheat lines carrying non-functional <i>SS2</i> homologues. Collectively, our findings uncover an evolutionarily conserved, silicon-dependent mechanism that regulates peduncle elongation and spike emergence in Triticeae crops like barley and wheat.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"24 8","pages":"4766-4779"},"PeriodicalIF":12.8,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.70666","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147630295","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":"PbrIDD2-PbrAPX14 Module Functions in the Ethylene-Mediated Ripening and Senescence Process of Pear Fruit","authors":"Libin Wang, Junpeng Niu, Xiaoyu Tan, Yuhua Xie, Li Jiang, Chen Huan, Xu Zhang, Weiqi Luo, Bing Xie, Xiaopu Ren, Guodong Wang, Yuanyuan Guo, Shaoling Zhang","doi":"10.1111/pbi.70664","DOIUrl":"10.1111/pbi.70664","url":null,"abstract":"<p>Endogenous H<sub>2</sub>O<sub>2</sub> participated in the ethylene-dependent ripening and senescence process of horticultural fruit as a secondary messenger; however, the molecular mechanism beneath such a phenomenon has not been fully clarified until recently. By a conjoint analysis of metabolite, enzyme activities, gene expression profiles in AsA-GSH cycle of ‘Kolar’ pear, <i>PbrAPX14</i> might act as a negative factor in the ethylene-mediated H<sub>2</sub>O<sub>2</sub> accumulation. PbrAPX14, located in cytosol, would reduce H<sub>2</sub>O<sub>2</sub> in vitro and in vivo, inhibit ethylene production, and thus fruit ripening and senescence. After analysing the expression profiles of the differentially expressed transcription factors (TFs) followed by experimental validation, the nuclear PbrIDD2 could directly bind to the <i>cis</i>-acting element (core motif: TTTGTCG) in <i>PbrAPX14</i> promoter, activate its expression and thus enhance the H<sub>2</sub>O<sub>2</sub>-scavenging capacity of fruit/calli, which was associated with the mitigated ethylene evolution and fruit ripening and senescence. Further study explored that the H<sub>2</sub>O<sub>2</sub>-mediated post-translational S-sulfenylation of Cys<sup>48</sup> residue in PbrAPX14, which mitigated its function, existed in vitro and in vivo, and was upregulated by ethylene, facilitating endogenous H<sub>2</sub>O<sub>2</sub> accumulation. Overall, our results implied that both transcriptional and post-translational regulation of PbrAPX14, which were (in)directly under the control of ethylene, functioned in pear ripening and senescence process via regulating endogenous H<sub>2</sub>O<sub>2</sub> level.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"24 8","pages":"4878-4896"},"PeriodicalIF":12.8,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.70664","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147751347","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}
Alessandro Occhialini, Xinlu Chen, Samantha A. Miller, Mohammad Majdi, Ivette A. Fuentes Quispe, Gabriella King, Feng Chen
{"title":"Evolution‐Inspired Engineering of Diterpene Biosynthesis via Chloroplast Genome Modification","authors":"Alessandro Occhialini, Xinlu Chen, Samantha A. Miller, Mohammad Majdi, Ivette A. Fuentes Quispe, Gabriella King, Feng Chen","doi":"10.1111/pbi.70729","DOIUrl":"https://doi.org/10.1111/pbi.70729","url":null,"abstract":"Terpenes constitute the largest and most structurally diverse class of plant secondary metabolites, with critical roles in plant‐environment interactions and broad industrial applications. Although nuclear genome engineering of terpene pathways has been extensively explored, chloroplast genome engineering remains largely undeveloped, with all reported studies restricted to the model plant <jats:italic>Nicotiana</jats:italic> . Here we report successful chloroplast genome engineering for diterpene production in the crop plant potato ( <jats:styled-content style=\"fixed-case\"> <jats:italic>Solanum tuberosum</jats:italic> </jats:styled-content> ) guided by evolutionary principles. First, we identified the <jats:italic>trnT/trnL</jats:italic> plastomic locus as a new transgene integration site with minimal integration‐associated growth penalties. Insertion of a bifunctional diterpene synthase gene from a fern that is absent in flowering plants into this plastomic site yielded transplastomic potato plants with successful production of new diterpenes, but with reduced growth. The co‐expression of an algal geranylgeranyl diphosphate synthase gene of chloroplast genome origin to enhance precursor supply restored normal growth while elevating diterpene production. Transplastomic plants were otherwise agronomically comparable to wild‐type. This work expands chloroplast engineering as a viable strategy for evolution‐inspired terpene pathway engineering in crop improvement and high‐value terpene production.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"51 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148498914","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}
Malihe Mirzaee, Corinne Best, Evelyn V. Wachowski, Pal Maliga
{"title":"RNA ‐Guided Engineering of the Chloroplast Genome Enabled by Plastid‐Expressed Guide RNAs","authors":"Malihe Mirzaee, Corinne Best, Evelyn V. Wachowski, Pal Maliga","doi":"10.1111/pbi.70728","DOIUrl":"https://doi.org/10.1111/pbi.70728","url":null,"abstract":"Our goal is to develop RNA‐guided engineering of the chloroplast genome using the CRISPR/Cas9 system. We designed chloroplast minigenes to obtain properly sized single guide RNAs (sgRNAs) in tobacco chloroplasts. The sgRNA 5′ end is defined by transcription from an rRNA operon promoter, and its 3′ end by processing a downstream tRNA (trnG) or a hepatitis delta virus (HDV) ribozyme. Cas9 is expressed from a nuclear gene and is targeted to chloroplasts by fusion to a transit peptide. Cas9 incorporated the sgRNA and introduced double‐strand breaks in the plastid DNA (ptDNA). We report here that the double‐strand DNA break in the <jats:italic>ndhA</jats:italic> and <jats:italic>rpoC1</jats:italic> genes was repaired by microhomology‐mediated end joining (MMEJ), resulting in deletions in the ptDNA. We further showed that nuclear‐expressed sgRNA can be delivered into chloroplasts by fusion with a viroid RNA, as one possible approach for RNA‐guided engineering of the ptDNA without direct chloroplast genome transformation. These results are the first step of RNA‐guided editing of the chloroplast genome in any crop.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"11 8 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148459339","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":"The E3 Ubiquitin Ligases SINA3 and SINA5 Control DEP2 Ubiquitination and Proteasomal Degradation to Regulate Grain Size and Weight in Rice","authors":"Hongming Wu, Xiejun Sun, Xin Wang, Chen Xie, Yingli Lv, Xiaoman You, Yu Zhang, Xiaohang Han, Yun Zhu, Yimin Lin, Yehui Xiong, Qibing Lin, Cailin Lei, Xiuping Guo, Shanshan Zhu, Zhijun Cheng, Yulong Ren, Ling Jiang, Jianmin Wan","doi":"10.1111/pbi.70723","DOIUrl":"https://doi.org/10.1111/pbi.70723","url":null,"abstract":"Grain size is a critical agronomic trait, yet the molecular mechanisms governing its determination in crops remain incompletely understood. While recent studies revealed that OsRING80 facilitates DENSE AND ERECT PANICLE 2 (DEP2) degradation to mediate immunity without impacting growth and development, our work identifies a distinct regulatory pathway controlling grain development. We demonstrate that two RING finger E3 ubiquitin ligases, SEVEN IN ABSENTIA 3 (SINA3) and SINA5, post‐translationally regulate the stability of DEP2 (also known as SRS1/EP2/OsRELA/SUG1) to modulate grain size. SINA3 and SINA5 physically interact with DEP2, specifically mediated through the C1 structural region of DEP2 containing a coiled‐coil domain. These E3 ligases promote K48‐linked polyubiquitination of DEP2, targeting it for proteasomal degradation. Liquid chromatography‐mass spectrometry (LC–MS) analysis identified six critical lysine residues (K399, K722, K746, K958, K962 and K1344) within DEP2 that are essential for its ubiquitylation and subsequent destabilization. Our genetic evidence further supports this regulatory module: knockout of <jats:italic>SINA3</jats:italic> and/or <jats:italic>SINA5</jats:italic> leads to DEP2 accumulation, concomitantly increasing grain size and 1000‐grain weight significantly, without altering other agronomic traits; conversely, overexpression of <jats:italic>SINA3</jats:italic> or <jats:italic>SINA5</jats:italic> reduces DEP2 protein levels and diminishes grain size and weight. Therefore, our study uncovers a novel post‐translational regulatory module where SINA3 and SINA5 control DEP2 stability to fine‐tune grain development. These findings present a promising strategy for optimizing grain yield by manipulating this post‐translational regulatory node.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"31 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148459340","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}
Shabnam Shamriz, Angelo Kaldis, Carly A. Charron, Jordan T. VanderBurgt, Christopher P. Garnham, Moussa S. Diarra, Rima Menassa
{"title":"Design and Immunogenicity of a Nanoparticle Combination Vaccine for Salmonella in Poultry","authors":"Shabnam Shamriz, Angelo Kaldis, Carly A. Charron, Jordan T. VanderBurgt, Christopher P. Garnham, Moussa S. Diarra, Rima Menassa","doi":"10.1111/pbi.70717","DOIUrl":"https://doi.org/10.1111/pbi.70717","url":null,"abstract":"<jats:styled-content style=\"fixed-case\"> <jats:italic>Salmonella enterica</jats:italic> </jats:styled-content> serovars ( <jats:italic>Salmonella</jats:italic> ) are common causes of bacterial gastroenteritis (salmonellosis) often associated with the consumption of poultry products. The control of <jats:italic>Salmonella</jats:italic> in broiler chickens is difficult because colonized birds may carry this pathogen undetected into the slaughterhouse and cause meat contamination. Poultry vaccines can mitigate colonization, and one promising production method is via plants. Iron is an essential nutrient for <jats:italic>Salmonella;</jats:italic> therefore, our goal was to exploit iron uptake systems as vaccine targets that could starve this pathogen of iron and thus prevent it from colonizing chickens. One challenge with this approach is that <jats:italic>Salmonella</jats:italic> possesses several iron acquisition proteins that are redundant in function. Therefore, we created nanoparticle‐based plant‐produced vaccine candidates against four different <jats:italic>Salmonella</jats:italic> iron acquisition proteins to create a multivalent vaccine that may be more effective than targeting a single protein. Extracellular antigenic peptides from each of these proteins were fused in tandem to the N‐terminus of the self‐assembling <jats:italic>Brucella</jats:italic> spp. lumazine synthase. These fusion constructs were then expressed in <jats:italic>Nicotiana benthamiana</jats:italic> plants. The resulting recombinant proteins were extracted, purified and characterized. The vaccine candidates administered individually or in combination elicited specific antibodies in mice and bound to the surface of <jats:italic>Salmonella,</jats:italic> indicating their potential in preventing <jats:italic>Salmonella</jats:italic> colonization in poultry.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"37 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148428815","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}
Xiao Yang, Shiwei Wei, Ge Jin, Li Zhang, Ran Du, Yajun Wang, Chengcheng Shen, Tao Huang, Guotao Huo, Jie Peng, Bo Song, Fangyuan Zhang, Victor Hugo Escalona Contreras, Lijun Luo, Yuejian Li, Francisco A. Tomas‐Barberan, Bin Liu, Qichang Yang
{"title":"Integrated Metabolomics and Selection Signal Analysis Provide Insights Into the Selection for Flavonol Biosynthesis Associated With Lettuce Quality Improvement","authors":"Xiao Yang, Shiwei Wei, Ge Jin, Li Zhang, Ran Du, Yajun Wang, Chengcheng Shen, Tao Huang, Guotao Huo, Jie Peng, Bo Song, Fangyuan Zhang, Victor Hugo Escalona Contreras, Lijun Luo, Yuejian Li, Francisco A. Tomas‐Barberan, Bin Liu, Qichang Yang","doi":"10.1111/pbi.70716","DOIUrl":"https://doi.org/10.1111/pbi.70716","url":null,"abstract":"Lettuce is a critical leafy vegetable consumed worldwide and is a substantial dietary source of health‐promoting compounds. Exploring changes in metabolism during lettuce domestication under artificial selection conditions is important to facilitate further breeding and cultivation for quality improvement. A liquid chromatography‐mass spectrometry‐based metabolomics approach was used to putatively identify 237 metabolites from 40 accessions, of which 130 were identified as metabolite identification level 1. Subsequently, 29 metabolites linked to lettuce quality improvement and their potential associated genes involved in lettuce domestication and differentiation were analysed. Muti‐omics approach showed that metabolites involved in flavonol biosynthesis are the main metabolic distinctions between wild and modern cultivars, which is attributable to the selection signal observed in <jats:italic>LsF3</jats:italic> ′ <jats:italic>H</jats:italic> , a key enzyme involved in the catalysis of flavonoid hydroxylation at the 3′‐position. These findings provide a comprehensive view of quality‐ and flavour‐related metabolite variation in lettuce, reveal the potential for quality improvement associated with flavonol biosynthesis, and offer valuable insights into the genetic basis for improving lettuce flavour and nutrition.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"147 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148428814","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}
Hongtao Zhang,Johnathan A Napier,Frederica L Theodoulou
{"title":"Assessing the Impact of Multigene Engineering on the Proteome: Omega-3 Camelina as a Case Study.","authors":"Hongtao Zhang,Johnathan A Napier,Frederica L Theodoulou","doi":"10.1111/pbi.70712","DOIUrl":"https://doi.org/10.1111/pbi.70712","url":null,"abstract":"","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"30 22 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148429145","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}
Elisabetta Mazzucotelli,Cristian Forestan,Gina Zastrow-Hayes,David Swarbreck,Yael Lev-Mirom,Emile Cavalet-Giorsa,Matteo Bozzoli,Anna Maria Mastrangelo,Daniela Marone,Vincent Ranwez,Johanna Girodolle,Victor Llaca,Kevin Fengler,Charlotte Harris,Helena Toegelová,Pavla Navrátilová,Primetta Faccioli,Francesca Desiderio,Ana Paola Valladares,Gemy Kaithakottil,Rachel L Rusholme-Pilcher,Manuel Spannagl,Heidrun Gundlach,Klaus F X Mayer,Victoria C Blake,Justin D Faris,Steven S Xu,Taner Z Sen,Eric Yao,Julio Isidro Y Sánchez,Chunyi Liu,Muhammad A Farooq,Sandra Stefanelli,Chiara Cappucci,Leah Oren,Tamar Eilam,Mario Giorgioni,Alessandra Stella,Barbara Lazzari,Massimiliano Lauria,Aldo Ceriotti,Raul Pirona,Elahe Tavakol,Valentyna Klymiuk,Jennifer Ens,Harmeet Singh Chawla,Sean Walkowiak,Nicola Pecchioni,Filippo M Bassi,Miguel Sanchez-Garcia,Gabriella Sonnante,Pasquale L Curci,Giovanni Giuliano,Giuseppe Aprea,Asher Pasha,Agata Gadaleta,Ilaria Marcotuli,Stefania Masci,Francesco Sestili,Samuela Palombieri,Davide Scaglione,Michele Morgante,Hana Šimková,Nicholas J Provart,Simon G Krattinger,Curtis J Pozniak,Nathalie Chantret,Anthony Hall,Assaf Distelfeld,Roberto Tuberosa,Marco Maccaferri,Luigi Cattivelli
{"title":"Durum Wheat cv. Svevo Reference Genome Rel.2.0: A Comprehensive Tool for Wheat Genomics.","authors":"Elisabetta Mazzucotelli,Cristian Forestan,Gina Zastrow-Hayes,David Swarbreck,Yael Lev-Mirom,Emile Cavalet-Giorsa,Matteo Bozzoli,Anna Maria Mastrangelo,Daniela Marone,Vincent Ranwez,Johanna Girodolle,Victor Llaca,Kevin Fengler,Charlotte Harris,Helena Toegelová,Pavla Navrátilová,Primetta Faccioli,Francesca Desiderio,Ana Paola Valladares,Gemy Kaithakottil,Rachel L Rusholme-Pilcher,Manuel Spannagl,Heidrun Gundlach,Klaus F X Mayer,Victoria C Blake,Justin D Faris,Steven S Xu,Taner Z Sen,Eric Yao,Julio Isidro Y Sánchez,Chunyi Liu,Muhammad A Farooq,Sandra Stefanelli,Chiara Cappucci,Leah Oren,Tamar Eilam,Mario Giorgioni,Alessandra Stella,Barbara Lazzari,Massimiliano Lauria,Aldo Ceriotti,Raul Pirona,Elahe Tavakol,Valentyna Klymiuk,Jennifer Ens,Harmeet Singh Chawla,Sean Walkowiak,Nicola Pecchioni,Filippo M Bassi,Miguel Sanchez-Garcia,Gabriella Sonnante,Pasquale L Curci,Giovanni Giuliano,Giuseppe Aprea,Asher Pasha,Agata Gadaleta,Ilaria Marcotuli,Stefania Masci,Francesco Sestili,Samuela Palombieri,Davide Scaglione,Michele Morgante,Hana Šimková,Nicholas J Provart,Simon G Krattinger,Curtis J Pozniak,Nathalie Chantret,Anthony Hall,Assaf Distelfeld,Roberto Tuberosa,Marco Maccaferri,Luigi Cattivelli","doi":"10.1111/pbi.70673","DOIUrl":"https://doi.org/10.1111/pbi.70673","url":null,"abstract":"Advancements in plant genome sequencing and assembly have enabled the production of increasingly accurate and contiguous genome sequences. Here, we present the chromosome-level assembly of the durum wheat (Triticum turgidum L. ssp. durum, cv. Svevo) reference genome produced using accurate long-reads, optical mapping and Hi-C. The new assembly (Svevo Rel.2.0) comprises 263 hybrid scaffolds with an N50 value of 112.3 Mb, arranged into 14 contiguous pseudomolecules spanning 10.4 Gb. The Svevo Rel.2.0 genome assembly was annotated using extensive short- and long-read RNA sequencing data obtained from 60 tissue/treatment combinations. The resulting annotation comprises 68 154 high-confidence protein-coding genes, which have been integrated into a comprehensive transcriptome atlas accessible through an eFP browser. Annotation was manually curated for storage protein gene families and for Leucine-Rich Repeat-Containing Receptor genes yielding 3763 LRR-CR loci. The genome assembly's accuracy and completeness were demonstrated by the correct reconstruction of the physical map of Tg1-B (Tenacious glumes 1), a locus controlling the free threshing trait located on chromosome 2B that was not assembled in the previous genome release (Svevo Rel.1.0). A wealth of 6621 QTLs/MTAs from the literature were mapped onto Svevo Rel.2.0 to identify QTL hotspots and trait-specific candidate genes. The ancestry of the durum genome to representative wild emmer populations from North-Eastern and Southern-Levant Fertile Crescent assessed by tracing haplotype transmission patterns revealed a clear mosaic pattern. This new durum reference genome, enhanced with advanced annotation and an expression atlas linked to QTLome data, is the most comprehensive tool available for durum wheat genomics.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"21 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148429146","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}