{"title":"The homoeolog-resolved assembly of the 40-Gb decaploid Thinopyrum ponticum genome reveals extensive homoeologous exchange and recombination, segmental allopolyploid organization, and allelic variations for wheat improvement.","authors":"Pingchuan Deng, Jingzhong Xie, Xuanzhao Li, Xiangqian Chen, He Dai, Zhengbao Xia, Jingli Fan, Yanzhen Wang, Tingdong Li, Qiaoling Luo, Chunhuan Chen, Jixin Zhao, Changyou Wang, Xinlun Liu, Xue Shi, Liang Wu, Xiaojun Nie, Qi Zheng, Zhensheng Li, Eduard Akhunov, Fei He, Wanquan Ji","doi":"10.1016/j.molp.2026.09.014","DOIUrl":"https://doi.org/10.1016/j.molp.2026.09.014","url":null,"abstract":"<p><p>The decaploid grass Thinopyrum ponticum (Th. ponticum, 2n = 10x = 70) is valuable for improving wheat resilience to biotic and abiotic stressors. However, the high level of ploidy and repetitive nature of its large genome present challenges for genome assembly. We used long-read sequencing and an iterative reassembly strategy to overcome partial haplotype collapse and generate a homoeolog-resolved 41.33-Gb decaploid genome assembly for this grass. Combined comparative genomic, phylogenetic, and k-mer analyses resolved its diploid ancestral origins. Genome-wide recombination-based evidence, corroborated by gametophytic genomic and multiple cytological analyses, further revealed extensive homoeologous exchange consistent with a segmental allopolyploid organization. Annotation of this assembly recovered 577,421 high-confidence genes, the largest gene repertoire reported among Triticeae genomes, including a 22-copy Fhb7 tandem gene cluster distributed across five chromosomes. A wheat-Th. ponticum introgression panel of 348 lines catalogued the beneficial allelic diversity captured in a long-term breeding program, revealing candidate regulators of blue aleurone and identifying an expanded Fhb7 gene cluster as a transferable Fusarium head blight resistance resource. These results provide insights into the structural basis of segmental allopolyploid genome stabilization and offer both a framework and extensive resources to study the basic mechanisms of hybrid introgression and recombination in polyploids.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":32.7,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112305","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 non-canonical DWARF3–OsCOX11-mediated mitochondrial ROS homeostasis pathway acts in parallel with core strigolactone signaling to promote rice blast resistance","authors":"Weijun Cui,Xuming Wang,Xiuli Liu,Hongjia Liu,Yuwen Lu,Fei Yan,Keke Yi,Jianping Chen,Jie Zhou","doi":"10.1016/j.molp.2026.09.012","DOIUrl":"https://doi.org/10.1016/j.molp.2026.09.012","url":null,"abstract":"Strigolactones (SLs) are a class of plant hormones with multifaceted roles in rice (Oryza sativa L.) growth and development. The F-box protein DWARF3 (D3) is a core component of the SL signalling pathway, coupling SL perception to the downstream responses. However, whether D3 also contributes to rice immunity and how it functions in this process remain unclear. Here, we analysed D3 allelic mutants carrying deletions in F-box- or C-terminal helix (CTH) domains. These mutants exhibited increased susceptibility to Magnaporthe oryzae, and differentially affected the expression of PHENYLALANINE AMMONIA LYASE genes and lignin accumulation, indicating that this canonical SL-regulated pathway contributes to, but does not fully account for, D3-mediated blast resistance. Yeast two-hybrid screening identified OsCOX11, a cytochrome c oxidase (COX) assembly factor, as a D3-interacting protein. D3 promotes the ubiquitination and degradation of OsCOX11, thereby modulating mitochondrial function and reactive oxygen species (ROS) accumulation during immune responses. Loss of D3 function resulted in increased COX activity, aberrant mitochondrial morphology, and compromised elicitor-induced ROS burst, particularly in the CTH-truncated line. Notably, rac-GR24 activated canonical SL signalling but did not measurably alter the D3–OsCOX11 interaction, OsCOX11 abundance, or COX activity under the tested conditions. Together, our findings identify a D3–OsCOX11 mitochondrial branch that operates in parallel with core D3–DWARF53 signalling and contributes to rice blast resistance.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"47 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149019703","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":"Structural Evolution of LEAFY Reveals DNA-Mediated Cooperativity and Dimerization Shifts at the Water-to-Land Transition","authors":"Leonie Verhage,Emmanuel Thévenon,Hicham Chahtane,Alice Jegou,Loïc Grandvuillemin,Max H. Nanao,Renaud Dumas,Chloe Zubieta,François Parcy","doi":"10.1016/j.molp.2026.09.009","DOIUrl":"https://doi.org/10.1016/j.molp.2026.09.009","url":null,"abstract":"The evolution of transcription factor (TF) DNA-binding specificity is a major driver of gene regulatory innovation. Unlike most TFs, which diversify through gene duplication and neofunctionalization, the plant-specific LEAFY (LFY) TF evolved novel binding specificities without extensive duplication. Here, we combine experimental structural determination and biochemical assays to reveal how LFY’s dimerization and DNA-binding preferences shifted during the water-to-land transition. We present crystal structures of the LFY DNA-binding domain (DBD) from the hornwort Nothoceros aenigmaticus and the alga Interfilum paradoxum bound to DNA, demonstrating two distinct dimerization mechanisms: one mediated by direct protein-protein interactions and another driven by DNA-mediated cooperativity. In the ancestral state, LFY likely bound DNA as a dimer through DNA-mediated cooperativity, with protein-protein dimerization emerging later, enforcing new DNA-binding preferences. Our findings support a revised evolutionary scenario for LFY, highlighting the dynamic interplay between protein-DNA and protein-protein interactions as key drivers of TF binding specificity. This work deepens our understanding of how structural adaptations in TFs underpin evolutionary transitions in gene regulation.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"5 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149019727","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":"Receptor-Like Kinase ZmRLK9 Functions as an Upstream ABA Signaling Factor Conferring Drought Resilience in Maize.","authors":"Haohao Wu, Zilong Zhang, Shiping Yang, Qin Huang, Shuqing Ye, Ning Qin, Bochen Zhao, Yijie Wang, Ziyang Wang, Jiafan He, Mengyuan Wang, Ying Xiao, Zhirui Yang, Shengxue Liu, Feng Qin","doi":"10.1016/j.molp.2026.09.010","DOIUrl":"https://doi.org/10.1016/j.molp.2026.09.010","url":null,"abstract":"<p><p>The phytohormone abscisic acid (ABA) plays a pivotal role in plant drought responses. Although a substantial amount of research has concentrated on intracellular ABA receptors and SnRK2 protein kinases as the central signaling components, how the extracellular ABA signal is transduced to this core pathway remains largely unknown. Here, through a genome-wide association study mapping drought resistance in maize at the flowering stage, we identify a 4,052-bp hAT transposon insertion upstream of a leucine-rich repeat receptor-like kinase gene, named ZmRLK9, that suppresses gene expression and compromises drought resilience. ZmRLK9 functions as a plasma membrane-localized receptor kinase that transduces the extracellular ABA signal to the core ABA pathway. Upon ABA treatment, ZmRLK9 phosphorylates and promotes the degradation of an F-box protein, ZmFBP1, thereby stabilizing the core ABA signaling kinases ZmSnRK2.9 and ZmSnRK2.10. Enhancing ZmRLK9 expression or knocking out ZmFBP1 significantly enhances drought resistance in maize at both seedling and flowering stages and increases grain yield under drought conditions in the field. Collectively, our findings reveal a previously unrecognized regulatory module that operates upstream of the core ABA signaling pathway and highlight ZmRLK9 and ZmFBP1 as promising genetic targets for breeding crops with enhanced drought resilience.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":32.7,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149025652","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":"From DNA to RNA to protein: pQTL mapping and Proteome-Wide Association Study reveal protein-level drivers of soybean traits","authors":"Delin Li,Zhan Li,Shiyu Guo,Qi Wang,Xinkang Feng,Hao Zhang,James C. Schnable,Ying-Hui Li,Li-Juan Qiu","doi":"10.1016/j.molp.2026.09.011","DOIUrl":"https://doi.org/10.1016/j.molp.2026.09.011","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":"31 1","pages":""},"PeriodicalIF":27.5,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149013585","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}