Molecular Plant最新文献

{"title":"Discovery of the cytochrome P450 monooxygenase prenyl cyclases that catalyze the final step of glyceollin biosynthesis in soybean.","authors":"Praveen Khatri, Kuflom Kuflu, Tim McDowell, Jie Lin, Nikola Kovinich, Sangeeta Dhaubhadel","doi":"10.1016/j.molp.2025.01.022","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.022","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075132","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":"GEFormer: a Genomic Prediction Method of Genotype-Environment Interaction in Maize by Integrating Gating Mechanism MLP and Linear Attention Mechanism.","authors":"Zhou Yao, Mengting Yao, Chuang Wang, Ke Li, Junhao Guo, Yingjie Xiao, Jianbing Yan, Jianxiao Liu","doi":"10.1016/j.molp.2025.01.020","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.020","url":null,"abstract":"<p><p>The integration of genotypic and environmental data can enhance the prediction accuracy of field traits of crops. The existing genomic prediction methods fail to consider the environmental factors and do not consider the real growing environment of crops, resulting in low genomic prediction accuracy. In this work, we propose a genotype-environment interaction genomic prediction method in maize, called GEFormer, based on integrating the gating mechanism MLP and linear attention mechanism. Firstly, it uses gated multilayer perceptron (gMLP) to extract the local and global features among SNPs. Then, the Omni-dimensional Dynamic Convolution is used to extract the dynamic and comprehensive features of multiple environmental factors within each day in the consideration of the real growth pattern of crops. The linear attention mechanism is used to capture the temporal features of environmental changes. Finally, it uses the gating mechanism to fuse the genomic and environmental features effectively. We validate the accuracy of GEFormer in predicting important agronomic traits of maize, rice and wheat in three experimental scenarios: untested genotypes in tested environments, tested genotypes in untested environments, untested genotypes in untested environments. Experimental results show that GEFormer outperforms six cutting-edge statistical learning methods and four machine learning methods. Furthermore, it shows great advantages in the experimental scenario of untested genotypes in untested environments. In addition, we used GEFormer into three real-world breeding applications: phenotype prediction in unknown environments, hybrid phenotype prediction using inbred population, and cross-population phenotype prediction. The results illustrate that GEFormer exhibiting better prediction performance in actual breeding scenarios, and it can be utilized to assist crop breeding.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066845","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":"Chloroplast State Transitions Modulate Nuclear Genome Stability via Cytokinin Signaling in Arabidopsis.","authors":"Yajun Zeng, Sujuan Duan, Yawen Wang, Zhifeng Zheng, Zeyi Wu, Meihui Shi, Manchun Wang, Lan Jiang, Xue Li, Hong-Bin Wang, Hong-Lei Jin","doi":"10.1016/j.molp.2025.01.021","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.021","url":null,"abstract":"<p><p>Activities of the chloroplasts and nucleus are coordinated by retrograde signaling, which has crucial roles in plant development and environmental adaptation. However, the connection between chloroplast status and nuclear genome stability is not well understood. Chloroplast state transitions allow the plant to balance the absorption capacity of the photosystems in an environment in which the light quality was changing. Here we demonstrate that abnormal chloroplast state transitions lead to instability of the nuclear genome and impaired plant growth. We observed increased DNA damage in the state transition-defective Arabidopsis (Arabidopsis thaliana) mutant stn7; this damage was triggered by cytokinin accumulation and activation of cytokinin signaling. We propose that cytokinin signaling promotes the competitive association of ARABIDOPSIS RESPONSE REGULATOR 10 (ARR10) with PROLIFERATING CELLULAR NUCLEAR ANTIGEN 1/2 (PCNA1/2), thereby inhibiting the binding of PCNA1/2 to nuclear DNA. This affects DNA replication, leading to replication-dependent genome instability. Treatment with 2,5-dibromo-3-methyl-6-isopropylbenzoquinone, which simulates the reduction of the plastoquinone pool during abnormal state transitions, increased the accumulation of ARABIDOPSIS HISTIDINE-CONTAINING PHOSPHOTRANSMITTER 1, a phosphotransfer protein involved in cytokinin signaling, and promoted the interaction of ARR10 with PCNA1/2, leading to DNA damage. These findings highlight the role of cytokinin signaling in coordinating chloroplast function and nuclear genome integrity during plant acclimation to environmental changes.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066843","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":"Graph-based pangenome provides insights into the structural variation and genetic basis of metabolic traits in potato.","authors":"Xiaoling Zhu, Rui Yang, Qiqi Liang, Yuye Yu, Tingting Wang, Li Meng, Ping Wang, Shaoyang Wang, Xianping Li, Qiongfen Yang, Huachun Guo, Qijun Sui, Qiang Wang, Hai Du, Qin Chen, Zhe Liang, Xuewei Wu, Qian Zeng, Binquan Huang","doi":"10.1016/j.molp.2025.01.017","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.017","url":null,"abstract":"<p><p>Potato is the world's most important nongrain crop. Here, we report that 29 genomes from Petota and Etuberosum sections were de novo assembled, and that 248 accessions of wild potatoes, landraces and modern cultivars were re-sequenced at > 25× depth to assess genetic diversity within the Petota section. Subsequently, a graph-based pangenome was constructed by using DM8.1 as the backbone integrated 194,330 nonredundant structural variants. To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits, LC-MS/MS was employed to obtain the metabolome of 157 accessions, and 9,321 SVs were detected to be significantly associated with 1,258 distinct metabolites via PAV-based metabolomics-GWAS analysis, including metabolites of flavonoids, phenolic acids and phospholipids. To facilitate the utilization of pangenome resources, a comprehensive platform, the potato pangenome database (PPDB, http://101.201.107.228:16666/), was developed for the potato community worldwide. Our study provides a comprehensive genomic resource that enables us to assess the genomic basis of agronomic and metabolic traits, and the genomic dataset resources will accelerate functional genomics studies and genetic improvements in potato.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052868","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":"DNA damage triggers heritable alterations in DNA methylation patterns in Arabidopsis.","authors":"Jinchao Li, Wenjie Liang, Xin-Qiang He, Weiqiang Qian","doi":"10.1016/j.molp.2025.01.019","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.019","url":null,"abstract":"<p><p>It has been hypothesized that DNA damage has the potential to induce DNA hypermethylation, contributing to carcinogenesis in mammals. However, there is no sufficient evidence to support that DNA damage can cause genome-wide DNA hypermethylation. Here, we demonstrated that DNA single-strand breaks with 3'-blocked ends (DNA 3'-blocks) can not only reinforce DNA methylation at normally methylated loci but also can induce DNA methylation at normally nonmethylated loci in plants. The CG and CHG hypermethylation tend to localize within gene bodies, with a significant proportion being de novo generated. In contrast, the CHH hypermethylation is concentrated in centromeric and pericentromeric regions, primarily being reinforced methylation. Mechanistically, DNA 3'-blocks regulate the DREAM complex to induce CG and CHG methylation. Moreover, they utilize the RdDM pathway to induce CHH hypermethylation. Intriguingly, repair of the DNA damage or blocking the DNA damage response can fully abolish CHH hypermethylation and partially rescue CHG hypermethylation but rarely alter CG hypermethylation, indicating that DNA damage-induced symmetric DNA methylation can serve as a form of genetic imprinting. Collectively, our results suggest that DNA damage is an important force driving the emergence and evolution of genomic DNA methylation levels and patterns in plants.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040166","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 typical NLR recognizes a family of structurally conserved effectors to confer plant resistance against adapted and non-adapted Phytophthora pathogens.","authors":"Xiaohua Dong, Xu Lu, Hai Zhu, Zhengxue Zhu, Peiyun Ji, Xianglan Li, Tianli Li, Xiong Zhang, Gan Ai, Daolong Dou","doi":"10.1016/j.molp.2025.01.018","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.018","url":null,"abstract":"<p><p>Plants possess remarkably durable resistance against non-adapted pathogens in nature. However, the molecular mechanisms underlying this resistance remain poorly understood, and it is unclear how the resistance is maintained without coevolution between hosts and the non-adapted pathogens. In this study, we used Phytophthora sojae (Ps), a non-adapted pathogen of N. benthamiana (Nb), as a model and identified an RXLR effector that determines Nb incompatibility to Ps. Knockout of this RXLR effector in Ps enables successful infection of Nb, leading us to name it AvrNb (Avirulence gene in Nb). A systematic screening of Nb NLR genes further revealed that NbPrf, previously reported to be a receptor of bacterial avirulence proteins, is the NLR protein responsible for mediating AvrNb recognition and initiating the hypersensitive response (HR). Mutation of NbPrf completely makes Nb compatible to Ps. We found that AvrNb is conserved among multiply Phytophthora pathogens, and these homologs also induce NbPrf-dependent HR. Remarkably, further inoculation assay showed that NbPrf is involved in plant immunity to two adapted Phytophthora pathogens, P. infestans and P. capsici. Our findings suggest that NbPrf represents a promising breeding resource for resistance to Phytophthora pathogens, and also demonstrate that the conserved effectors present in both adapted and non-adapted pathogens may provide sufficient selective pressure to maintain the remarkably durable incompatibility between plants and non-adapted pathogens.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040158","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 genomic variation map provides insights into potato evolution and key agronomic traits.","authors":"Qun Lian, Yingying Zhang, Jinzhe Zhang, Zhen Peng, Weilun Wang, Miru Du, Hongbo Li, Xinyan Zhang, Lin Cheng, Ran Du, Zijian Zhou, Zhenqiang Yang, Guohui Xin, Yuanyuan Pu, Zhiwen Feng, Qian Wu, Guochao Xuanyuan, Shunbuer Bai, Rong Hu, Sónia Negrão, Glenn J Bryan, Christian W B Bachem, Yongfeng Zhou, Ruofang Zhang, Yi Shang, Sanwen Huang, Tao Lin, Jianjian Qi","doi":"10.1016/j.molp.2025.01.016","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.016","url":null,"abstract":"<p><p>Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop, which requires a deep understanding of potato domestication and differentiation. Here, we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants. Using the variome map, we discovered the reshaping of tuber transcriptome during potato domestication, characterized genome-wide differentiation between landrace groups Stenotomum and Phureja, and identified a jasmonic acid biosynthetic gene possibly affecting tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for biosynthesis of antinutritional steroidal glycoalkaloids (SGAs), and a Dehydration Responsive Element Binding (DREB) transcription factor conferring increased average tuber weight. In addition, genome similarity and group-specific SNP analyses indicated tetraploid potatoes originated from the diploid S. tuberosum group Stenotomum. These findings shed light on the evolutionary trajectory of potato domestication and improvement, providing a solid foundation for advancing hybrid potato breeding practices.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040156","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":"New molecular chaperone roles for CO₂ assimilation in early land plants.","authors":"Julie L McDonald, Robert H Wilson","doi":"10.1016/j.molp.2025.01.015","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.015","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008776","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":"NTRC mediates the coupling of chloroplast redox rhythm with nuclear circadian clock in plant cells.","authors":"Seol Ki Paeng, Seong Dong Wi, Ho Byoung Chae, Su Bin Bae, Kieu Anh Thi Phan, Min Gab Kim, Dae-Jin Yun, Woe-Yeon Kim, C Robertson McClung, Sang Yeol Lee","doi":"10.1016/j.molp.2025.01.014","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.014","url":null,"abstract":"<p><p>The intricate interplay between cellular circadian rhythms, primarily manifested in the chloroplast redox oscillations-characterized by diel hyperoxidation/reduction cycles of 2-Cys Peroxiredoxins-and the nuclear transcription/translation feedback loop (TTFL) machinery within plant cells, demonstrates a remarkable temporal coherence. However, the molecular mechanisms underlying the integration of these circadian rhythms remain elusive. Here, we elucidate that the chloroplast redox protein, NADPH-dependent thioredoxin reductase type-C (NTRC), modulates the integration of the chloroplast redox rhythms and nuclear circadian clocks by regulating intracellular levels of reactive oxygen species and sucrose. In NTRC-deficient ntrc mutants, the perturbed temporal dynamics of cytosolic metabolite pools substantially attenuated the amplitude of CIRCADIAN CLOCK ASSOCIATED-1 (CCA1) mRNA oscillation, while maintaining its inherent periodicity. In contrast, these fluctuations extended the period and ameliorated the amplitude of GIGANTEA (GI). In alignment with its regulatory role, the chloroplast redox rhythm and TTFL-driven nuclear oscillators are severely disrupted in ntrc plants. The impairments are rescued by NTRC expression, but not by the catalytically inactive NTRC(C/S) mutant, indicating that NTRC's redox activity is essential for synchronizing intracellular circadian rhythms. In return, the canonical nuclear clock component, TIMING OF CAB EXPRESSION-1 (TOC1), regulates the diel chloroplast redox rhythm by controlling NTRC expression, as evidenced by the redox cycle of chloroplast 2-Cys Peroxiredoxins. This reciprocal regulation suggests a tight coupling between chloroplast redox rhythms and nuclear oscillators. Consequently, our research has successfully identified NTRC as a key circadian modulator, elucidating the intricate connection between the metabolite-dependent chloroplast redox rhythm and the temporal dynamics of nuclear canonical clocks.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008777","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":"Getting the SCOOP on peptide ligands that regulate leaf senescence.","authors":"Judy A Brusslan","doi":"10.1016/j.molp.2025.01.013","DOIUrl":"https://doi.org/10.1016/j.molp.2025.01.013","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008773","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}