Molecular Plant最新文献_第9页

Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design. 对现代栽培品种的大规模基因组和表型组分析有助于未来的水稻育种设计。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-13 DOI: 10.1016/j.molp.2025.03.007

Xiaoding Ma, Hao Wang, Shen Yan, Chuanqing Zhou, Kunneng Zhou, Qiang Zhang, Maomao Li, Yaolong Yang, Danting Li, Peng Song, Cuifeng Tang, Leiyue Geng, Jianchang Sun, Zhiyuan Ji, Xianjun Sun, Yongli Zhou, Peng Zhou, Di Cui, Bing Han, Xin Jing, Qiang He, Wei Fang, Longzhi Han

{"title":"Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design.","authors":"Xiaoding Ma, Hao Wang, Shen Yan, Chuanqing Zhou, Kunneng Zhou, Qiang Zhang, Maomao Li, Yaolong Yang, Danting Li, Peng Song, Cuifeng Tang, Leiyue Geng, Jianchang Sun, Zhiyuan Ji, Xianjun Sun, Yongli Zhou, Peng Zhou, Di Cui, Bing Han, Xin Jing, Qiang He, Wei Fang, Longzhi Han","doi":"10.1016/j.molp.2025.03.007","DOIUrl":"10.1016/j.molp.2025.03.007","url":null,"abstract":"Modern cultivated rice plays a pivotal role in global food security. China accounts for nearly 30% of the world's rice production and has developed numerous cultivated varieties over the past decades that are well adapted to diverse growing regions. However, the genomic bases underlying the phenotypes of these modern cultivars remain poorly characterized, limiting the exploitation of this vast resource for breeding specialized, regionally adapted cultivars. In this study, we constructed a comprehensive genetic variation map of modern rice using resequencing datasets from 6044 representative cultivars from five major rice-growing regions in China. Our genomic and phenotypic analyses of this diversity panel revealed regional preferences for specific genomic backgrounds and traits, such as heading date, biotic/abiotic stress resistance, and grain shape, which are crucial for adaptation to local conditions and consumer preferences. We identified 3131 quantitative trait loci associated with 53 phenotypes across 212 datasets under various environmental conditions through genome-wide association studies. Notably, we cloned and functionally verified a novel gene related to grain length, OsGL3.6. By integrating multiple datasets, we developed RiceAtlas, a versatile multi-scale toolkit for rice breeding design. We successfully utilized the RiceAtlas breeding design function to rapidly improve the grain shape of the Suigeng4 cultivar. These valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"651-668"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625475","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}

引用次数: 0

Mobilizing Triticeae diversity from gene banks to farmer's field. 将小麦品种从基因库转移到农民的田间。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-08 DOI: 10.1016/j.molp.2025.03.006

Awais Rasheed, Jindong Liu, Rudi Appels, Zhonghu He

引用次数: 0

The near-complete genome assembly of pickling cucumber and its mutation library illuminate cucumber functional genomics and genetic improvement. 酸黄瓜近全基因组组装及其突变文库为黄瓜功能基因组学和遗传改良提供了新的思路。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-04 DOI: 10.1016/j.molp.2025.03.001

Yao Tian, Kui Li, Tonghui Li, Wudi Gai, Jie Zhou, Xing Wang Deng, Yan Xue, Yun Deng, Hang He, Xingping Zhang

引用次数: 0

Plant PAQR-like sensors activate heterotrimeric G proteins to confer resistance against multiple pathogens. 植物paqr样传感器刺激异源三聚体g蛋白，赋予对多种病原体的抗性。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-01 DOI: 10.1016/j.molp.2025.02.006

Houxiao Zhang, Yuzhu Zhang, Quanlin Li, Fengsheng Hao, Gary Stacey, Dongqin Chen

{"title":"Plant PAQR-like sensors activate heterotrimeric G proteins to confer resistance against multiple pathogens.","authors":"Houxiao Zhang, Yuzhu Zhang, Quanlin Li, Fengsheng Hao, Gary Stacey, Dongqin Chen","doi":"10.1016/j.molp.2025.02.006","DOIUrl":"10.1016/j.molp.2025.02.006","url":null,"abstract":"Human adiponectin receptors (AdipoRs) and membrane progestin receptors (mPRs, members of the progestin and adipoQ receptor [PAQR] family) are seven-transmembrane receptors involved in the regulation of metabolism and cancer development, which share structural similarities with G protein-coupled receptors. Plant PAQR-like sensors (PLSs) are homologous to human PAQRs but their molecular functions remain unclear. In this study, we found that PLSs associate with cell surface receptor-like kinases through KIN7 and positively regulate plant immune responses, stomatal defense, and disease resistance. Moreover, PLSs activate heterotrimeric G proteins (Gαβγ) to transduce immune signals and regulate the exchange of GDP for GTP on GPA1. Further analyses revealed that the immune function of PLSs is conserved in rice and soybean and contributes to resistance against multiple diseases. Notably, heterologous expression of human AdipoRs in Arabidopsis replicates the immune functions of PLSs. Collectively, our findings demonstrate that PLSs are key modulators of plant immunity via the G-protein pathway and highlight the potential application of human genes in enhancing plant disease resistance.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"639-650"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Graph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato. 基于图谱的泛基因组为马铃薯代谢性状的结构变异和遗传基础提供了新的思路。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-01-27 DOI: 10.1016/j.molp.2025.01.017

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

{"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":"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.","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}

引用次数: 0

SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing. SuperDecode：一个用于分析基因组编辑引起的突变的集成工具包。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-04 DOI: 10.1016/j.molp.2025.03.002

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

{"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":"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.","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}

引用次数: 0

A genomic variation map provides insights into potato evolution and key agronomic traits. 基因组变异图提供了对马铃薯进化和关键农艺性状的深入了解。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-01-23 DOI: 10.1016/j.molp.2025.01.016

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

{"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":"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.","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}

引用次数: 0

NTRC's novel role: Bridging chloroplast redox oscillations and nuclear circadian clock. NTRC的新作用：连接叶绿体氧化还原振荡和核生物钟。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-03 DOI: 10.1016/j.molp.2025.03.003

Francisco Javier Cejudo

引用次数: 0

A comprehensive omics resource and genetic tools for functional genomics research and genetic improvement of sorghum. 高粱功能基因组学研究和遗传改良的综合组学资源和遗传工具。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-07 DOI: 10.1016/j.molp.2025.03.005

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

{"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":"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.","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}

引用次数: 0

DNA damage triggers heritable alterations in DNA methylation patterns in Arabidopsis. DNA损伤引发拟南芥DNA甲基化模式的遗传改变

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-24 DOI: 10.1016/j.molp.2025.01.019

Jinchao Li, Wenjie Liang, Xin-Qiang He, Weiqiang Qian

{"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":"10.1016/j.molp.2025.01.019","url":null,"abstract":"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. In this study, we demonstrated that DNA single-strand breaks with 3' blocked ends (DNA 3' blocks) not only can 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 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, these results suggest that DNA damage is an important force driving the emergence and evolution of genomic DNA methylation levels and patterns in plants.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"501-512"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","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}

引用次数: 0