Molecular Plant最新文献

{"title":"SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing.","authors":"Fuquan Li, Xiyu Tan, Shengting Li, Shaotong Chen, Lin Liu, Jingjing Huang, Gufeng Li, Zijun Lu, Jinwen Wu, Dongchang Zeng, Yanqiu Luo, Xiaoou Dong, Xingliang Ma, Qinlong Zhu, Letian Chen, Yao-Guang Liu, Chengjie Chen, Xianrong Xie","doi":"10.1016/j.molp.2025.03.002","DOIUrl":"10.1016/j.molp.2025.03.002","url":null,"abstract":"<p><p>Genome editing using CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) or other systems has become a cornerstone of numerous biological and applied research fields. However, detecting the resulting mutations by analyzing sequencing data remains time consuming and inefficient. In response to this issue, we designed SuperDecode, an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies. SuperDecode comprises three modules, DSDecodeMS, HiDecode, and LaDecode, each designed to automatically decode mutations from Sanger, high-throughput short-read, and long-read sequencing data, respectively, from targeted PCR amplicons. By leveraging specific strategies for constructing sequencing libraries of pooled multiple amplicons, HiDecode and LaDecode facilitate large-scale identification of mutations induced by single or multiplex target-site editing in a cost-effective manner. We demonstrate the efficacy of SuperDecode by analyzing mutations produced using different genome editing tools (CRISPR/Cas, base editing, and prime editing) in different materials (diploid and tetraploid rice and protoplasts), underscoring its versatility in decoding genome editing outcomes across different applications. Furthermore, this toolkit can be used to analyze other genetic variations, as exemplified by its ability to estimate the C-to-U editing rate of the cellular RNA of a mitochondrial gene. SuperDecode offers both a standalone software package and a web-based version, ensuring its easy access and broad compatibility across diverse computer systems. Thus, SuperDecode provides a comprehensive platform for analyzing a wide array of mutations, advancing the utility of genome editing for scientific research and genetic engineering.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"690-702"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567749","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 structural variations 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":"10.1016/j.molp.2025.01.017","url":null,"abstract":"<p><p>Potato is the world's most important nongrain crop. In this study, to assess genetic diversity within the Petota section, 29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes, landraces, and modern cultivars were re-sequenced at >25× depth. Subsequently, a graph-based pangenome was constructed using DM8.1 as the backbone, integrating194,330 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 structural variants (SVs) were detected to be significantly associated with 1,258 distinct metabolites via PAV (presence and absence variations)-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), was developed. Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato, which will accelerate functional genomics studies and genetic improvements in potato.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"590-602"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","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":"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":"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. In the present study, 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. We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional 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 that tetraploid potatoes originated from the diploid Solanum 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":"570-589"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","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":"NTRC's novel role: Bridging chloroplast redox oscillations and nuclear circadian clock.","authors":"Francisco Javier Cejudo","doi":"10.1016/j.molp.2025.03.003","DOIUrl":"10.1016/j.molp.2025.03.003","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"560-562"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557491","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 comprehensive omics resource and genetic tools for functional genomics research and genetic improvement of sorghum.","authors":"Chengxuan Chen, Fengyong Ge, Huilong Du, Yuanchang Sun, Yi Sui, Sanyuan Tang, Zhengwei Shen, Xuefeng Li, Huili Zhang, Cuo Mei, Peng Xie, Chao Li, Sen Yang, Huimin Wei, Jiayang Shi, Dan Zhang, Kangxu Zhao, Dekai Yang, Yi Qiao, Zuyong Luo, Li Zhang, Aimal Khan, Baye Wodajo, Yaorong Wu, Ran Xia, Chuanyin Wu, Chengzhi Liang, Qi Xie, Feifei Yu","doi":"10.1016/j.molp.2025.03.005","DOIUrl":"10.1016/j.molp.2025.03.005","url":null,"abstract":"<p><p>Sorghum, the fifth most important food crop globally, is a source of silage forage, fiber, syrup, and biofuel. Moreover, it is widely recognized as an ideal model crop for studying stress biology becaused of its ability to tolerate multiple abiotic stresses, including high salt-alkali conditions, drought, and heat. However, functional genomics studies on sorghum have been challenging, primarily due to the limited availability of genetic resources and effective genetic transformation techniques. In this study, we developed the Sorghum Genomics and Mutation Database (SGMD), aiming to advance the genetic understanding of sorghum. Our effort encompassed a telomere-to-telomere genome assembly of an inbred sorghum line, E048, yielding 729.46 Mb of sequence data representing the complete genome. Alongside the high-quality sequence data, a gene expression atlas covering 13 distinct tissues was developed. We constructed a saturated ethyl methane sulfonate mutant library comprising 13,226 independent mutants. Causal genes in chlorosis and leafy mutants from the library were easily identified by leveraging the MutMap and MutMap+ methodologies, demonstrating the powerful application of this library for identifying functional genes. To facilitate sorghum research, we performed whole-genome sequencing of 179 M₂ mutant lines, resulting in 2,291,074 mutations that covered 97.54% of all genes. In addition, an Agrobacterium-mediated sorghum transformation platform was established for gene function studies. In summary, this work establishes a comprehensive platform and provides valuable resources for functional genomics investigations and genetic improvement of sorghum.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"703-719"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586357","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":"Comparative spatial transcriptomics reveals root dryland adaptation mechanism in rice and HMGB1 as a key regulator.","authors":"Liyuan Zhong, Leping Geng, Yimeng Xiang, Xuanmin Guang, Le Cao, Jiawei Shi, Weikun Li, Jianglin Wang, Weiming He, Liyu Huang, Feng Yang, Yi-Xuan Bai, Sunil Kumar Sahu, Xing Guo, Shilai Zhang, Gengyun Zhang, Xun Xu, Fengyi Hu, Wanneng Yang, Huan Liu, Yu Zhao, Jun Lyu","doi":"10.1016/j.molp.2025.04.001","DOIUrl":"https://doi.org/10.1016/j.molp.2025.04.001","url":null,"abstract":"<p><p>Drought severely threatens food security, and its detrimental effects will be exacerbated by climate change in many parts of the world. Rice production is water consuming and particularly vulnerable to drought stress. A special rice ecotype called upland rice specifically adapts to dryland mainly through its robust root system. However, the molecular and developmental mechanism underlying this adaption has remained elusive. Here, by comparing the root development between upland and irrigated rice phenotypically and cytologically, we identified key developmental phenotypes that distinguish upland rice. We further generate spatial transcriptomic atlases for coleoptilar nodes and root tips to explore the molecular differences in crown root formation and development between upland and irrigated rice, uncovering promising genes for enhancing drought resistance. Among the identified genes, HMGB1, a transcriptional regulator, functions as a key factor that elongates and thickens roots in upland rice and enhances drought resistance. Our study uncovered spatially resolved transcriptomic features in upland rice root that contribute to its adaptation to dryland conditions, providing valuable genetic resources for breeding drought resilient rice.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803843","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":"Two E-clade Protein Phosphatase 2Cs enhance ABA signaling by dephosphorylating ABI1 in Arabidopsis.","authors":"Ya Zhang, Liyuan Han, Junjie Liu, Miao Chang, Chuanling Li, Jian-Xiu Shang, Zhiping Deng, Wenqiang Tang, Yu Sun","doi":"10.1016/j.molp.2025.03.019","DOIUrl":"https://doi.org/10.1016/j.molp.2025.03.019","url":null,"abstract":"<p><p>ABA INSENSITIVE 1 (ABI1) and ABI2 are co-receptors of the phytohormone abscisic acid (ABA). Studies have demonstrated that phosphorylation of multiple amino acids on ABI1/2 augments their ability to inhibit ABA signaling in planta. However, it is currently unknown whether there exists a mechanism to regulate the dephosphorylation of ABI1/2 that enhances the plant's sensitivity to ABA. In this study, we identified two protein phosphatases, designated ABI1 Dephosphorylating E clade PP2C 1 (ADEP1) and ADEP2, that interact with ABI1/2. Mutants lacking ADEP1, ADEP2, or both (adep1/2) exhibited reduced sensitivity to ABA-inhibited seed germination, root growth and ABA-induced stomatal closure. Additionally, ABA-induced accumulation of ABI5 protein and the expression of downstream target genes were reduced in the adep1/2 mutant compared to the wild-type. These findings suggest that ADEP1/2 function as positive regulators of the ABA signaling pathway. Mass spectrometry analysis and two-dimensional electrophoresis identified Ser¹¹⁷ as a major ABA-induced phosphorylation site on ABI1 protein. ADEP1/2 can dephosphorylate Ser¹¹⁷, leading to the destabilization of ABI1 protein and increased sensitivity to ABA in plants. Moreover, ABA treatment decreases the abundance of ADEP1/2 proteins. Overall, our study discovers two novel regulatory proteins that modulate ABA signaling and provides new insights into the regulatory network that fine-tune plant ABA responses.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764452","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 dual-targeted transcription factor BAI1 orchestrates nuclear and plastid gene transcription in land plants.","authors":"Jing Qin, Yelin Shan, Hao Liu, Zhangzhi Xue, Yike Xie, Guoxin Yuan, Yiming Zou, Xiaonuan Hao, Yunpeng Zhu, Xuan Shen, Meng Li, Xu Wang, Puyuan Liu, Jinxiu Xu, Yuhua Wang, Peng Zhao, Yuan Chen, Yi Zhu, Min Xu, Ming Yue, Aigen Fu, Weiguo Zhang, Beibei Li","doi":"10.1016/j.molp.2025.03.018","DOIUrl":"https://doi.org/10.1016/j.molp.2025.03.018","url":null,"abstract":"<p><p>Coordinated gene transcription in plastid and nucleus is essential for the photosynthetic apparatus assembly during chloroplast biogenesis. Despite identification of several transcription factors regulating the transcription of nuclear-encoded photosynthetic genes,no transcription factor regulating plastid gene transcription has been discovered. Here we report that BAI1 (\"albino\" in Chinese), a nucleus-plastid dual-targeted C2H2-type zinc finger transcription factor in Arabidopsis, positively regulates and orchestrates the transcription of nuclear and plastid genes. The knockout of BAI1 leads to the blockage of chloroplast formation, albino seedling, and lethality. In plastid, BAI1 is a newly identified functional component of the pTAC (transcriptionally active chromosome complex), which physically interacts with another pTAC component, pTAC12/PAP5/HMR to enable the effective assembly of PEP (plastid-encoded RNA polymerase) complex. The transcript levels of investigated PEP-dependent genes were reduced in the bai1 mutant, while the accumulation of NEP (nuclear-encoded RNA polymerase)-dependent transcripts was increased, indicating that BAI1 plays a vital role in maintaining PEP activity. BAI1 directly binds to the promoter regions of RbcSs, a nuclear gene, and RbcL, a plastid gene, to activate their expression for efficient RubisCO assembly. AtBAI1 homologs TaBAI1, GmBAI1a and GmBAI1b from both monocot and dicot can fully complement the defects of Arabidopsis bai1 mutant. In contrast, PpBAI1, from Physcomitrium patens, only partially complements the bai1 mutant. The phylogenetic analysis of BAI1 and HMR elucidated that both components originated from late-diverging streptophyte algae, following the conservative evolutionary path during plant terrestrialization. In summary, this work unveils a BAI1-mediated transcription regulatory mechanism synchronizing transcription of nuclear and plastid genes, which is required for hybrid photosynthetic complex assembly and could be an intrinsic feature facilitating plant terrestrialization.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764449","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":"RAPID LEAF FALLING 1 facilitates chemical defoliation and mechanical harvesting in cotton.","authors":"Bing Zhang, Dandan Yue, Bei Han, Danfan Bao, Xiao Zhang, Xuyang Hao, Xin Lin, Keith Lindsey, Longfu Zhu, Shuangxia Jin, Maojun Wang, Haijiang Xu, Mingwei Du, Yu Yu, Xianlong Zhang, Xiyan Yang","doi":"10.1016/j.molp.2025.03.017","DOIUrl":"https://doi.org/10.1016/j.molp.2025.03.017","url":null,"abstract":"<p><p>Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission through defoliant remains unsolved. In this study, through single-nucleus mRNA sequencing (snRNA-seq) of the abscission zone (AZ) from cotton petiole, we meticulously constructed a transcriptomic atlas and identified two newly-formed cell types, abscission cells and protection layer cells in cotton petiole AZ after defoliant treatment. GhRLF1 (RAPID LEAF FALLING 1), as one of the members encoding cytokinin oxidase/dehydrogenase (CKX) gene family, was identified as key marker gene unique to the abscission cells following defoliant treatment. Overexpression of GhRLF1 resulted in reduced cytokinin accumulation and accelerated leaf abscission. Conversely, CRISPR/Cas9-mediated loss of GhRLF1 function appeared to delay this process. Its interacting regulators, GhWRKY70, acting as \"Pioneer\" activator, and GhMYB108, acting as \"Successor\" activator, orchestrate a sequential modulation GhWRKY70/GhMYB108-GhRLF1-cytokinin (CTK) within the AZ to regulate cotton leaf abscission. GhRLF1 not only regulates leaf abscission but also reduces cotton yield. Consequently, transgenic lines exhibiting rapid leaf falling and requiring less defoliant, while maintaining unaffected cotton yield, were developed for mechanical harvesting. This was achieved using a defoliant-induced petiole-specific promoter proPER21, to drive GhRLF1 (proPER21::RLF1). This pioneering biotechnology offers a new strategy for the chemical defoliation of machine-harvested cotton, ensuring stable production and reducing leaf debris in harvested cotton, thereby enhancing environmental sustainability.</p>","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753674","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":"Reprogrammable design of DELLA as a strategy to mitigate alkaline-heat stress for sustainable agriculture.","authors":"Jie Hu, Hui Liu, Xiuhua Gao, Xiangdong Fu","doi":"10.1016/j.molp.2025.03.015","DOIUrl":"https://doi.org/10.1016/j.molp.2025.03.015","url":null,"abstract":"","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":""},"PeriodicalIF":17.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753676","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}