{"title":"Telomere-to-telomere genome assembly of linseed (Linum usitatissimum L.) for functional genomics and accelerated genetic improvement","authors":"Hemant Kumar Yadav, Neha Singh, Babita Singh, Vikender Kaur, Samir V. Sawant","doi":"10.1111/pbi.70183","DOIUrl":"https://doi.org/10.1111/pbi.70183","url":null,"abstract":"Linseed (<i>Linum usitatissimum</i> L.), a member of the Linaceae family, is a versatile crop valued for its oil, fibre, nutritional and medicinal applications. Recognized as a superfood, linseed is rich in omega-3 fatty acid (~55%), lignans, high-quality proteins, dietary fibre and bioactive secondary metabolites. Previously published genome assemblies of linseed are quite fragmented and non-contiguous. In this study, we present a telomere-to-telomere (T2T) chromosome-scale genome assembly of the Indian linseed variety T397 using advanced sequencing approaches. The assembly comprises ~595 Mb of genomic sequences, with a scaffold N50 of 32.86 Mb, spanning 15 chromosomes, including 29 telomeres and 15 centromeres. A total of 34 572 protein-encoding genes were predicted with an average length of 2980.7 bp and an average of 5.0 exons per gene. Gene family analysis determines a considerable number of unique genes in linseed and its close relationship with <i>Manihot esculenta</i> and <i>Ricinus communis.</i> The higher expression of oleosin and FAD3 genes in linseed highlights their roles in oil accumulation and enrichment for omega-3 fatty acid. The metabolites found in the seeds were enriched for the biosynthesis of unsaturated fatty acids. Various potential key structural genes and transcription factors that regulate oil metabolism especially unsaturated fatty acids biosynthesis has been identified. Overall, the present study provides the potential genomic resources for accelerated genetic studies and improvement of linseed.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"23 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320391","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":"A module with multiple transcription factors positively regulates powdery mildew resistance in grapevine.","authors":"Xiuming Zhang,Qihan Zhang,Yanxun Zhu,Yichu Zhang,Xiaoxiao Yan,Chunlei Guo,Min Gao,Zhi Li,Yijie Zhao,Hua Lu,Xiping Wang","doi":"10.1111/pbi.70196","DOIUrl":"https://doi.org/10.1111/pbi.70196","url":null,"abstract":"Erysiphe necator, the causal agent of powdery mildew (PM), is a fungal pathogen that can severely reduce crop yields. In this study, stable overexpression and silencing demonstrated that the transcription factor VqWRKY46 was identified as a positive regulator of PM resistance in grapevine. This enhanced resistance was associated with increased callose deposition and hypersensitive response cell death. We also demonstrated that VqLIMYB specifically activated VqWRKY46 expression by binding to a CAGTTA motif in its promoter. Moreover, VqWRKY46 interacted with VqNF-YC9 and formed homodimers, positively regulating VqNF-YC9 expression by directly binding to three W-box motifs in its promoter. Additionally, DAP-Seq analysis identified VqDSC1, a TIR-NB-LRR resistance protein, as a downstream target of VqWRKY46 in grapevine. Further analysis indicated that VqWRKY46 directly bound to Wbox1 in the VqDSC1 promoter to upregulate its expression, whereas VqNF-YC9 did not bind. Interestingly, the interaction between VqNF-YC9 and VqWRKY46 enhanced the DNA binding activity of VqWRKY46 to promote the expression of VqDSC1. Furthermore, overexpressing VqLIMYB, VqNF-YC9, and VqDSC1 in Arabidopsis and/or instantaneous transformation in grapes showed that they are positive regulators of PM resistance. Collectively, our findings uncover a novel regulatory module (VqLIMYB-VqWRKY46/VqNF-YC9-VqDSC1) that mediates grapevine resistance to E. necator. This study provides new insights into the molecular basis of grapevine resistance to PM and highlights potential targets for breeding disease-resistant grapevines.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"12 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320032","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}
Vanika Garg,Rutwik Barmukh,Yan Huang,Annapurna Chitikineni,Kristy Hobson,Bicheng Yang,Yong Jia,Shengnan Bi,Sukhjiwan Kaur,Muhammad Ahsan Asif,Matthew Hayden,Sally Norton,Darshan L Sharma,Kadambot H M Siddique,Xin Liu,Chengdao Li,Rajeev K Varshney
{"title":"An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement.","authors":"Vanika Garg,Rutwik Barmukh,Yan Huang,Annapurna Chitikineni,Kristy Hobson,Bicheng Yang,Yong Jia,Shengnan Bi,Sukhjiwan Kaur,Muhammad Ahsan Asif,Matthew Hayden,Sally Norton,Darshan L Sharma,Kadambot H M Siddique,Xin Liu,Chengdao Li,Rajeev K Varshney","doi":"10.1111/pbi.70192","DOIUrl":"https://doi.org/10.1111/pbi.70192","url":null,"abstract":"Chickpea (Cicer arietinum L.) is an important legume crop that has been subjected to intensive breeding, resulting in limited genetic diversity. Australia is the world's second largest producer and the leading exporter of chickpea; the genomic architecture of its cultivars remains largely unexplored. This knowledge gap hinders efforts to enhance their genetic potential for production, protection, and stress adaptation. To address this, we generated high-quality genome assemblies and annotations for 15 leading Australian chickpea cultivars using single-tube long-fragment read technology. The pan-genome analysis identified 34 345 gene families, including 13 986 dispensable families enriched for genes associated with key agronomic traits. Comparative genomic analysis revealed ~2.5 million single-nucleotide polymorphisms, nearly 200 000 insertions/deletions, and over 280 000 structural variations. These variations were found in key flowering time genes, seed weight-related genes, and disease resistance genes, providing insights into the genetic diversity underlying these critical traits. Haplotype analysis of key genes within the 'QTL-hotspot' region revealed the absence of superior haplotypes in Australian cultivars. Validation using Kompetitive allele-specific PCR markers confirmed these findings, highlighting the need to introduce beneficial haplotypes from diverse accessions to enhance drought tolerance in Australian chickpea cultivars. The genomic resources generated in this study provide valuable insights into chickpea genetic diversity and offer potential avenues for crop improvement.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"70 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320225","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":"A chaperonin BnaC01.CCT8 contributes to silique length and seed weight by affecting auxin and jasmonic acid signalling in Brassica napus.","authors":"Zhaoyang Qu,Ze Tian,Liqing Wei,Chao Wang,Lieqiong Kuang,Jiaqi Yan,Furong Wang,Nian Wang,Jinxing Tu,Xinfa Wang,Hanzhong Wang,Xiaoling Dun","doi":"10.1111/pbi.70184","DOIUrl":"https://doi.org/10.1111/pbi.70184","url":null,"abstract":"Seed weight (SW), which is directly influenced by silique length (SL), is a critical agronomic trait significantly affecting both the quality and yield of rapeseed. In this study, a shorter silique length (ssl) mutant was generated through ethyl methane sulfonate mutagenesis, exhibiting reduced SL and SW compared to the wild type. Utilizing a map-based cloning approach, BnaC01.CCT8, a member of the chaperonin containing T-complex polypeptide-1 (CCT) family, was identified as the gene responsible for restoring the ssl phenotype. A missense mutation from alanine to valine (A507V) in BnaC01.CCT8 was identified as crucial for its functional activity, as evidenced by the genetic complementation of BnaC01.CCT8 and BnaC01.CCT8A507V in the Arabidopsis cct8-2 background. Moreover, overexpression of BnaC01.CCT8 in Brassica napus significantly enhanced SL, SW and seed yield per plant. Conversely, CRISPR/Cas9-mediated bnac01.cct8 knockout lines exhibited reduced SL and SW. Transcriptome analysis and hormone content detection indicated that BnaC01.CCT8 positively regulated SL and SW primarily by modulating auxin and jasmonic acid signalling, thereby affecting the length of epidermal cells in the silique wall. Furthermore, BnaC01.CCT8 interacted with BnaA09.ARF18 (AUXIN-RESPONSE FACTOR 18), contributing to the regulation of SL and SW, while the A507V mutation disrupted this interaction. Haplotype analysis demonstrated that several SNP differences in BnaC01.CCT8 were significantly associated with variations in SL and SW among germplasm resources, revealing superior alleles of BnaC01.CCT8. The identification and functional analysis of BnaC01.CCT8 provide new insights into the mechanisms regulating SL and SW and present a valuable target for the genetic enhancement of rapeseed yield.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"44 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320098","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}
Chidambareswaren Mahadevan, Emma C Watts, Kaijie Zheng, Shi-Jian Song, Renier A L van der Hoorn
{"title":"Polyphenol oxidase silencing avoids protein cross-linking and enzymatic browning in Nicotiana benthamiana leaf extracts.","authors":"Chidambareswaren Mahadevan, Emma C Watts, Kaijie Zheng, Shi-Jian Song, Renier A L van der Hoorn","doi":"10.1111/pbi.70202","DOIUrl":"https://doi.org/10.1111/pbi.70202","url":null,"abstract":"","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324029","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}
Xuefeng Wei,Guangjin Fan,Song Yang,Xianchao Sun,Lin Cai
{"title":"Morphology effect of a novel biocompatible nucleic acid delivery nanosystem of g-C3N4@dsRNA for application in plant gene expression and plant virus disease protection.","authors":"Xuefeng Wei,Guangjin Fan,Song Yang,Xianchao Sun,Lin Cai","doi":"10.1111/pbi.70189","DOIUrl":"https://doi.org/10.1111/pbi.70189","url":null,"abstract":"Delivery of exogenous nucleic acid to intact plants is a desirable but challenging technology due to the dominant transport barrier posed by the plant cell wall. Here, we found that three different morphologies of g-C3N4 nanomaterials synthesized from urea can assist in the delivery of exogenous nucleic acids into mature leaf cells of Nicotiana benthamiana. Among these, g-C3N4 carbon dots (CDs) showed a higher ability to deliver exogenous nucleic acid compared to nanoporous and g-C3N4 nanosheets. The delivery ability of exogenous dsRNA and plasmid DNA by g-C3N4 could also be restrained by stomatal closure and the endocytosis pathways in plant cells. Furthermore, the coupling of g-C3N4 CDs with dsCP (CDs@dsCP), which is the dsRNA matching a specific fragment of the Coat protein-encoding gene of TMV, resulted in a superior antiviral effect compared with other morphologies of g-C3N4@dsRNAs and other loaded dsRNAs, which match Replicase, RNA-dependent Replicase or Movement protein of TMV. Significantly, a single spray of CDs@dsCP provided virus protection for at least 5 days. In addition, the g-C3N4 CDs and g-C3N4 CDs@dsRNA had no adverse effects on plant growth and development. Overall, our study presents a novel biocompatible and convenient tool for gene expression or gene silencing in intact plant leaves by spraying g-C3N4 nanomaterials encapsulated with DNA or dsRNA, the efficiency of which is affected by the morphology of the g-C3N4 nanomaterial, stomatal state and plant endocytosis pathway, and a highly promising solution for plant virus disease, which is an unsolved problem in plant disease control.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"15 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320030","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":"Exploring potential strategies for haploid induction based on double fertilization in plants.","authors":"Tengyu Li,Chenlei Wang,Jingwen Pan,Javaria Tabusam,Yan Li,Jinbo Yao,Wei Chen,Yazhong Wang,Wei Gao,Junkang Rong,Zeeshan Ahmad,Andreas Houben,Shouhong Zhu,Shuangxia Jin,Yongshan Zhang","doi":"10.1111/pbi.70197","DOIUrl":"https://doi.org/10.1111/pbi.70197","url":null,"abstract":"Haploid induction (HI), an indispensable procedure in doubled haploid breeding, has attracted increasing attention in crop genetic improvement due to its ability to rapidly fix desirable traits in a homozygous state, thereby shortening the breeding cycle. However, HI has only been successfully implemented in a limited number of crops, and its underlying mechanisms remain largely enigmatic. This review summarizes five potential HI routes based on previous findings and the key events during the process of double fertilization in flowering plants. Among these HI methods, we suggest that sperm DNA fragmentation and ectopic expression of embryogenesis activator, as straightforward avenues for discovering new HI-related genes. We also emphasize that the combination of genome editing techniques with HI is a promising strategy to accelerate crop improvement and doubled haploid breeding. We envision that the proposed directions can pave the way for improving and deepening our understanding of HI mechanisms.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"240 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320031","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":"Editing cis-elements of OsPHO1;2 improved phosphate transport and yield in rice","authors":"Kanika Maurya, Balaji Mani, Bhagat Singh, Ujjwal Sirohi, Aime Jaskolowski, Sandeep Sharma, Harsha Vardhan Tatiparthi, Satendra Kumar Mangrauthia, Renu Pandey, Yves Poirier, Jitender Giri","doi":"10.1111/pbi.70165","DOIUrl":"https://doi.org/10.1111/pbi.70165","url":null,"abstract":"Increasing grain yield is the primary goal of crop improvement, which is globally affected by the low availability of soil phosphate (Pi). Overexpressing Pi transporters to enhance Pi uptake often results in Pi toxicity and growth retardation. Despite advances in genetic engineering, targeting the <i>cis-</i>regulatory motifs of Pi transporters remains underexplored for understanding plant mechanisms and improving Pi status. Here, we demonstrate that the excision of the transcription inhibitor motif from the promoter of the Pi transporter <i>OsPHO1;2</i> enhances its expression and increases root-to-shoot Pi transport, leading to improved grain yield. Through <i>in silico</i> and DNA-protein interaction studies, we show the role of the OsWRKY6 transcription factor in negatively regulating <i>OsPHO1;2</i> expression by binding to the <i>cis</i>-regulatory element (<i>W-box</i>) present in its promoter. The <i>oswrky6</i> knockout lines exhibit higher <i>OsPHO1;2</i> expression and improved shoot Pi levels. Furthermore, we engineered the <i>OsPHO1;2</i> promoter to precisely remove the <i>W-box</i> and enhance <i>OsPHO1;2</i> expression. Phenotypic and physiological evaluations at the vegetative stage indicate that <i>OsPHO1;2</i> promoter-edited (<i>OsPHO1;2:PE</i>) lines have increased shoot length, plant biomass and greater root-to-shoot Pi export under both low and normal P conditions. Notably, the <sup>33</sup>P uptake assay reveals that <i>OsPHO1;2:PE</i> lines display enhanced root Pi uptake, supported by higher expression of root-associated Pi transporters (<i>OsPHTs</i>). An extensive agronomic assessment shows that <i>OsPHO1;2:PE</i> lines achieve increased seed and panicle numbers, thereby raising yield without affecting seed quality. Our findings provide valuable insights into the potential of promoter editing to improve Pi use and enhance crop yield.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"36 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144305492","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}
Dipak Gayen, Sunil Kumar, Pragya Barua, Nilesh Vikram Lande, Subhasis Karmakar, Amit K. Dey, Saurabh Gayali, Tushar Kanti Maiti, Kutubuddin Ali Molla, Snehal Murumkar, Subhra Chakraborty, Niranjan Chakraborty
{"title":"OsDUF2488 acts synergistically with OsPrx1.1, regulates ROS metabolism and promotes dehydration tolerance in rice","authors":"Dipak Gayen, Sunil Kumar, Pragya Barua, Nilesh Vikram Lande, Subhasis Karmakar, Amit K. Dey, Saurabh Gayali, Tushar Kanti Maiti, Kutubuddin Ali Molla, Snehal Murumkar, Subhra Chakraborty, Niranjan Chakraborty","doi":"10.1111/pbi.70182","DOIUrl":"https://doi.org/10.1111/pbi.70182","url":null,"abstract":"Stress-mediated regulation of energy metabolism and its relation to plant adaptation remain largely unknown. Mitochondrial redox potential is greatly influenced by stress-induced reactive oxygen species (ROS); therefore, we mapped the dehydration-induced alterations in the mitochondrial proteome of a resilient rice cultivar, Rasi, generating a proteome map representing the largest inventory of dehydration-responsive mitochondrial proteins from any plant species. Quantitative proteomic analysis led to the identification of an array of dehydration-responsive proteins (DRPs), associated with various cellular functions, conceivably impinging on the molecular mechanism of adaptation. One DRP identified in the mitochondrial proteome was yeast cadmium factor 54 (YCF54-like), also known as DUF (domain of unknown function) and hereafter referred to as OsDUF2488. We demonstrated that OsDUF2488 localises to mitochondria and preferentially interacts with peroxiredoxin, OsPrx1.1. Overexpression of OsDUF2488 in rice caused enhanced tolerance to dehydration and oxidative stress, while CRISPR/Cas9 knockout mutants of OsDUF2488 showed hypersensitivity to dehydration. Upon exposure to dehydration, OsDUF2488 could rescue mitochondrial dysfunction, contributing to increased ATP production in OsDUF2488-overexpressing rice. Coexpression of OsDUF2488 and OsPrx1.1 in yeast demonstrated a mutual effect on enhanced ROS catabolism, suggesting a cross-kingdom adaptive response of OsDUF2488. Our findings suggest that OsDUF2488 acts synergistically with OsPrx1.1 to regulate redox homeostasis and promote stress tolerance in rice.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"11 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144305514","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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