Plant Communications最新文献

{"title":"Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement.","authors":"Zehou Liu,Fan Yang,Hongshen Wan,Cao Deng,Wenjing Hu,Xing Fan,Jirui Wang,Manyu Yang,Junyan Feng,Qin Wang,Ning Yang,Li Cai,Ying Liu,Hao Tang,Shizhao Li,Jiangtao Luo,Jianmin Zheng,Ling Wu,Ennian Yang,Zongjun Pu,Jizeng Jia,Jun Li,Wuyun Yang","doi":"10.1016/j.xplc.2024.101131","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101131","url":null,"abstract":"The allotetraploid wild grass Aegilops ventricosa (2n=4X=28, genome DvDvNvNv) has been recognized as an important germplasm resource for wheat improvement due to its ability to tolerate biotic stresses. Especially 2NvS segment from Aegilops ventricosa, as a stable and effective resistance source, has greatly contributed to wheat improvement. The 2NvS/2AS translocation is a prevalent chromosomal translocation between common wheat and wild relatives, ranking just behind the 1B/1R translocation in importance for modern wheat breeding. Here, we assembled a high-quality chromosome-level reference genome of Ae. ventricosa RM271 with a total length of 8.67 Gb. Phylogenomic analyses revealed that the progenitor of the Dv subgenome of Ae. ventricosa was Ae. tauschii ssp. tauschii (genome DD); in contrast, the progenitor of the D subgenome of bread wheat (Triticum aestivum L.) was Ae. tauschii ssp. strangulata (genome DD). The oldest polyploidization time of Ae. ventricosa occurred ∼0.7 million years ago. The Dv subgenome of Ae. ventricosa was less conserved than the D subgenome of bread wheat. Construction of a graph-based pangenome of 2AS/6NvL (originally known as 2NvS) segments from Ae. ventricosa and other genomes in the Triticeae enables us identifying candidate resistance genes sourced from Ae. ventricosa. We identified 12 nonredundant introgressed segments from the Dv and Nv subgenomes using a large winter wheat collection representing the full diversity of the wheat European genetic pool, and 29.40% of European wheat varieties inherited at least one of these segments. The high-quality RM271 reference genome will provide a basis for cloning key genes, including the Yr17-Lr37-Sr38-Cre5 resistance gene cluster in Ae. ventricosa, and facilitate the full use of elite wild genetic resources to accelerate wheat improvement.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":10.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142188539","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":"Regulatory Networks of Coresident Subgenomes during Rapid Fiber Cell Elongation in Upland Cotton.","authors":"Lan Yang,Wenqiang Qin,Xi Wei,Rui Liu,Jiaxiang Yang,Zhi Wang,Qingdi Yan,Yihao Zhang,Wei Hu,Xiao Han,Chenxu Gao,Jingjing Zhan,Baibai Gao,Xiaoyang Ge,Fuguang Li,Zhaoen Yang","doi":"10.1016/j.xplc.2024.101130","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101130","url":null,"abstract":"Cotton, an intriguing plant species shaped by polyploidization, evolution, and domestication, holds particular interest due to the complex mechanisms governing fiber traits across its two subgenomes. However, the regulatory elements or transcriptional networks between subgenomes during fiber elongation remain elusive. Here, we analyzed 1,462 cotton fiber samples to reconstruct gene expression regulatory networks influencing fiber cell elongation. Inter-subgenomic eQTLs largely dictate gene transcription, with a notable tendency for the D subgenome to regulate A subgenome eGenes. This regulation showcases synchronized homoeologous gene expression driven by colocalized eQTLs and divergent patterns that diminish genetic correlations, thus leading to preferential expression in the A and D subgenomes. Hotspot456 emerged as a key regulator of fiber initiation and elongation, and artificial selection of trans-eQTLs in hotspot456 positively regulating KCS1 has facilitated cell elongation. To elucidate the roles of trans-eQTL in improved fiber breeding, experimentation confirmed the inhibition of GhTOL9 by a specific trans-eQTL via GhWRKY28, which negatively impacts fiber elongation. We propose a model where the GhWRKY28-GhTOL9 module, through the Endosomal Sorting Complex Required for Transport pathway, regulates this process. This research significantly advances our understanding of cotton's evolutionary, domestication processes, and the intricate regulatory mechanisms underlying significant plant traits.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":10.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142188540","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":"AcRLK2P-1, an LRR receptor protein kinase gene from Agropyron cristatum, confers leaf rust resistance in wheat.","authors":"Shirui Xu,Xiajie Ji,Haiming Han,Jinpeng Zhang,Shenghui Zhou,Baojin Guo,Xinming Yang,Xiuquan Li,Xiaomin Guo,Taiguo Liu,Lihui Li,Weihua Liu","doi":"10.1016/j.xplc.2024.101132","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101132","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":10.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142188506","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":"OsRbohI Is the Indispensable NADPH Oxidase for Molecular Patterns Induced Reactive Oxygen Species Production in Rice.","authors":"Zhifang Zhao,Aiqing Sun,Wenfeng Shan,Xinhang Zheng,Ying Wang,Lu Bai,Yuchen Xu,Zhuo An,Xiaoyi Wang,Yuanmeng Wang,Jiangbo Fan","doi":"10.1016/j.xplc.2024.101129","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101129","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":10.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142188541","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":"Rice E3 ubiquitin ligases: From key modulators of host immunity to potential breeding application.","authors":"Yuqing Yan, Hui Wang, Yan Bi, Fengming Song","doi":"10.1016/j.xplc.2024.101128","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101128","url":null,"abstract":"<p><p>To combat pathogen attacks, plants have developed a highly advanced immune system, which requires tight regulation to initiate robust defense responses while preventing autoimmunity simultaneously. The ubiquitin-proteasome system (UPS), responsible for degrading excess or misfolded proteins, exerts vital roles in ensuring strong and effective immune responses. E3 ligases, as key UPS components, have been extensively documented in rice immunity through modulating the ubiquitination and degradation of downstream substrates involved in various immune signaling pathways. Here, we summarize the crucial roles of rice E3 ligases in both pathogen/microbe/damage-associated molecular pattern-triggered immunity and effector-triggered immunity, highlight the molecular mechanisms of E3 ligases in rice immune signaling, and emphasize the functions of E3 ligases as targets of pathogen effectors for pathogenesis. We also discuss potential strategies for application of the immunity-associated E3 ligases in breeding disease-resistant rice varieties without growth penalty. This review thus provides comprehensive and updated understanding on the sophisticated and interconnected regulatory functions of E3 ligases in rice immunity and its balancing with growth and development.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142156639","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 and exploiting the rice phytobiome to tackle climate change challenges.","authors":"Seyed Mahdi Hosseiniyan Khatibi, Niña Gracel Dimaano, Esteban Veliz, Venkatesan Sundaresan, Jauhar Ali","doi":"10.1016/j.xplc.2024.101078","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101078","url":null,"abstract":"<p><p>The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past ten years has dramatically advanced the understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly on major crops such as rice. Taking into account the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss the interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Converging the gigantic datasets and complex information on the rice phytobiome and its application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142134412","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":"Lr34/Yr18/Sr57/Pm38 confers broad-spectrum resistance to fungal diseases via transport of sinapyl alcohol for cell wall lignification in wheat.","authors":"Yichen Zhang, Guang Chen, Yiming Zang, Sridhar Bhavani, Bin Bai, Wei Liu, Miaomiao Zhao, Yikeng Cheng, Shunda Li, Wei Chen, Wenhao Yan, Hailiang Mao, Handong Su, Ravi P Singh, Evans Lagudah, Qiang Li, Caixia Lan","doi":"10.1016/j.xplc.2024.101077","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101077","url":null,"abstract":"<p><p>Widely known pleiotropic adult plant resistance (PAPR) gene, Lr34 encodes an ATP-binding cassette transporter and plays an important role in breeding wheat for enhancing resistance against multiple fungal diseases. Despite its recognized significance, the mechanism underlying Lr34 in pathogen defense remains largely elusive. Our study demonstrated that wheat lines harboring the Lr34res allele exhibit thicker cell walls and enhanced resistance to fungal penetration compared to lines lacking Lr34res. Transcriptome and metabolite profiling revealed that the lignin biosynthetic pathway was repressed in lr34 mutants, indicating a disruption in cell wall lignification. Furthermore, our investigation uncovered the hypersensitivity of lr34 mutant lines to sinapyl alcohol, a major monolignol crucial for cell wall lignification. Yeast accumulation and efflux assays confirmed that Lr34 protein functions as a sinapyl alcohol transporter. Both genetic and virus-induced gene silencing (VIGS) experiments revealed that the disease resistance conferred by Lr34 could be enhanced with the addition of the TaCOMT-3B gene, which is responsible for biosynthesis of sinapyl alcohol. Collectively, our findings provide novel insights into the role of Lr34 in disease resistance, through mediating sinapyl alcohol transport and cell wall deposition. Moreover, TaCOMT-3B plays a synergistic role in the Lr34 facilitated defensive lignification in adult wheat plants against multiple fungal pathogens.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142134413","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 TATA-box binding protein-associated factor TAF12b facilitates the degradation of type-B response regulators to negatively regulate cytokinin signaling.","authors":"Liu-Ming Guo, Jing Li, Pan-Pan Qi, Jie-Bing Wang, Hussein Ghanem, Ling Qing, Heng-Mu Zhang","doi":"10.1016/j.xplc.2024.101076","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101076","url":null,"abstract":"<p><p>Cytokinins (CKs) are one of important classes of plant hormones essential for plant growth and development. The TATA-box binding protein-associated factor 12b (TAF12b) is involved in cytokinin (CK) signaling, but its molecular and biochemical mechanisms remain unclear. In this study, TAF12b of Nicotiana benthamiana (NbTAF12b) was found to mediate CK response by directly interacting with type-B response regulators (B-RRs), which are positive regulators of CK signaling, and inhibiting their transcriptional activities. The co-factor specifically facilitated the proteasomal degradation of non-phosphorylated B-RRs by recruiting the KMD family of F-box proteins. Such interactions between TAF12b and B-RRs also occur in other plant species. Genetic transformation experiments further showed that overexpression of NbTAF12b attenuates the CK-hypersensitive phenotype conferred by NbRR1 overexpression. Taken together, these results suggest a conserved mechanism that TAF12b negatively regulates CK responses through promoting 26S proteasome-mediated degradation of B-RRs degradation in multiple plant species, which provides novel insights into the regulatory network of CK signaling in plants.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127289","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 Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in Yuxingcao.","authors":"Zhengting Yang, Fayin He, Yingxiao Mai, Sixian Fan, Yin An, Kun Li, Fengqi Wu, Ming Tang, Hui Yu, Jian-Xiang Liu, Rui Xia","doi":"10.1016/j.xplc.2024.101075","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101075","url":null,"abstract":"<p><p>Houttuynia cordata Thunb., also known as Yuxingcao in Chinese, is a perennial herb in the Saururaceae family. It is highly regarded for its medicinal properties, particularly in treating respiratory infections and inflammatory conditions, as well as boosting the human immune system. However, the lack of genomic information has hindered research on the functional genomics and potential improvements of H. cordata. In this study, we present the assembly of a near-complete genome of H. cordata and investigate the biosynthesis pathway of flavonoids, specifically quercetin, using genomics, transcriptomics, and metabolomics analysis. The genome of H. cordata diverged from Saururus chinensis around 33.4 million years ago and consists of 2.24 Gb with 76 chromosomes (4n = 76), which underwent three whole-genome duplication (WGD) events. These WGDs played a crucial role in shaping H. cordata's genome and influencing gene families associated with its medicinal properties. Through metabolomics and transcriptomics analysis, we identified key genes involved in the β-oxidation process for houttuynin biosynthesis, one of the volatile oils responsible for its fishy-smell. Additionally, utilizing the reference genome, we effectively identified genes involved in flavonoid biosynthesis, particularly quercetin metabolism in H. cordata. This discovery has paramount implications for understanding the regulatory mechanisms of active pharmaceutical ingredient production in traditional Chinese medicine. Overall, the high-quality genome of H. cordata serves as a crucial resource for future functional genomics research and provides a solid foundation for genetic improvement of H. cordata for the benefit of human health.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127206","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":"Environmental genome-wide association studies across precipitation regimens reveal that the E3 ubiquitin ligase MBR1 regulates plant adaptation to rainy environments.","authors":"Simone Castellana, Paolo Maria Triozzi, Matteo Dell'Acqua, Elena Loreti, Pierdomenico Perata","doi":"10.1016/j.xplc.2024.101074","DOIUrl":"https://doi.org/10.1016/j.xplc.2024.101074","url":null,"abstract":"<p><p>In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis, understanding the mechanisms underlying local adaptation in plants is of paramount importance for the conservation of species. As the frequency and intensity of extreme precipitation events increase, so are the flooding events resulting from soil water saturation. The deriving onset of hypoxic stress is one of the leading causes of crop damage and yield loss. By combining genomics and remote sensing data, today it is possible to probe natural plant populations that have evolved in different rainfall regimes and look for molecular adaptation to hypoxia. Here, using an environmental genome-wide association study (eGWAS) on 934 non-redundant georeferenced Arabidopsis ecotypes, we have identified functional variants for the gene MED25 BINDING RING-H2 PROTEIN 1 (MBR1). This is a ubiquitin-protein ligase that regulates MEDIATOR25 (MED25), part of a multiprotein complex that interacts with transcription factors which act as key drivers of the hypoxic response in Arabidopsis, namely the RELATED TO AP2 proteins, RAP2.2 and RAP2.12. Through experimental validation, we show that natural variants of MBR1 have a differential impact on the stability of MED25 and, in turn, on hypoxia tolerance. This study also highlights the pivotal role of the MBR1/MED25 module in establishing a comprehensive hypoxic response. Our findings show that molecular candidates for plant environmental adaptation can be effectively mined from large datasets. This thus supports the need for the integration of forward and reverse genetics with robust molecular physiology validation of the outcomes.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114664","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}