发布求助
文献互助 智能选刊 最新文献

Cold Spring Harbor protocols最新文献

筛选
英文 中文
Sampling and Analysis of the Maize Microbiome. 玉米微生物组的取样和分析。
Cold Spring Harbor protocols Pub Date : 2025-10-01 DOI: 10.1101/pdb.top108463
Jason G Wallace, Alonso Favela, Sierra Raglin
{"title":"Sampling and Analysis of the Maize Microbiome.","authors":"Jason G Wallace, Alonso Favela, Sierra Raglin","doi":"10.1101/pdb.top108463","DOIUrl":"10.1101/pdb.top108463","url":null,"abstract":"<p><p>Maize is an important plant for both global food security and genetics research. As the importance of microorganisms to plant health is becoming clearer, there is a growing interest in understanding the relationship between maize and its associated microbiome; i.e., the collection of microorganisms living on, around, and inside the plant. The ultimate goal of this research is to use these microbial communities to support more robust and sustainable maize production. Here, we provide an overview of recent progress in the field of maize microbiome research. We discuss the major microbiome compartments (rhizosphere, phyllosphere, and endosphere) and known functions of the microbiome. We also review the methods currently available to study the maize microbiome and its functions, and discuss how to carry out maize microbiome experiments, including both a general workflow (suitable for most microbiome analyses) and maize-specific experimental considerations.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.top108463"},"PeriodicalIF":0.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sampling Maize (Zea mays) Seed Endophytes. 玉米（Zea mays）种子内生菌采样。
Cold Spring Harbor protocols Pub Date : 2025-10-01 DOI: 10.1101/pdb.prot108582
Jason G Wallace, Daniel Laspisa
{"title":"Sampling Maize (<i>Zea mays</i>) Seed Endophytes.","authors":"Jason G Wallace, Daniel Laspisa","doi":"10.1101/pdb.prot108582","DOIUrl":"10.1101/pdb.prot108582","url":null,"abstract":"<p><p>For most farmers, the production of maize grain is the ultimate goal of the entire field season. From the point of view of plant microbiome studies, seeds are particularly interesting in that they are the only avenue for vertical transmission of microbes from parent to offspring, though microbes can also enter maize seeds via wounds or silks. Although the presence of seed endophytes is well documented, their role, if any, in seed health and their effects on the next generation of plants are largely unknown. This protocol describes the isolation of seed endophytes. Its primary focus is properly sterilizing the seed surface, followed by grinding to release the endophytes. The end product is a cell suspension suitable for either culturing or DNA analysis.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108582"},"PeriodicalIF":0.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Preparation of Illumina 16s Amplicon Sequencing Libraries with Peptide Nucleic Acids (PNAs) for the Analysis of Maize-Associated Microbiomes. 用多肽核酸 (PNA) 制备用于分析玉米相关微生物组的 Illumina 16s 扩增片段测序文库。
Cold Spring Harbor protocols Pub Date : 2025-10-01 DOI: 10.1101/pdb.prot108583
Jason G Wallace, Holly Griffis
{"title":"Preparation of Illumina 16s Amplicon Sequencing Libraries with Peptide Nucleic Acids (PNAs) for the Analysis of Maize-Associated Microbiomes.","authors":"Jason G Wallace, Holly Griffis","doi":"10.1101/pdb.prot108583","DOIUrl":"10.1101/pdb.prot108583","url":null,"abstract":"<p><p>One of the most common methods to survey bacterial communities is targeted amplification of the hypervariable regions of the 16s rRNA gene followed by sequencing. This protocol details Illumina library preparation of such amplicons from communities isolated from maize. We include both staggered PCR primers to improve Illumina base calling and peptide nucleic acids (PNAs) to reduce the presence of plant organelles. Primers are designed with Illumina adapter sequences for the addition of sample-specific indexes (barcodes). We also briefly discuss alternative primer sets, including ones that directly discriminate against plant organelles or that amplify different organisms (e.g., fungal internal transcribed spacer [ITS] sequences).</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108583"},"PeriodicalIF":0.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sampling the Maize (Zea mays) Leaf Microbiome. 玉米（Zea mays）叶片微生物组取样。
Cold Spring Harbor protocols Pub Date : 2025-10-01 DOI: 10.1101/pdb.prot108581
Jason G Wallace
{"title":"Sampling the Maize (<i>Zea mays</i>) Leaf Microbiome.","authors":"Jason G Wallace","doi":"10.1101/pdb.prot108581","DOIUrl":"10.1101/pdb.prot108581","url":null,"abstract":"<p><p>The microbiota of maize leaves can be beneficial or detrimental to the host. Foliar diseases are the most obvious detrimental impact of the leaf microbiome, though more subtle effects of the normal (nondisease) community are an active area of research. This protocol describes two specific methodologies to sample the maize leaf microbiome: one sampling the surface (epiphyte) microbiome and one sampling the interior (endophyte) microbiome. Each method begins with collected leaf tissue and finishes with a cell suspension suitable for either isolating live microbes or extracting DNA for sequencing.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108581"},"PeriodicalIF":0.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sampling Root-Associated Microbiome Communities of Maize (Zea mays). 玉米（Zea mays）根相关微生物群落采样。
Cold Spring Harbor protocols Pub Date : 2025-10-01 DOI: 10.1101/pdb.prot108580
Alonso Favela, Sierra Raglin, Jason G Wallace
{"title":"Sampling Root-Associated Microbiome Communities of Maize (<i>Zea mays</i>).","authors":"Alonso Favela, Sierra Raglin, Jason G Wallace","doi":"10.1101/pdb.prot108580","DOIUrl":"10.1101/pdb.prot108580","url":null,"abstract":"<p><p>The soil microbiome of maize shapes its fitness, sustainability, and productivity. Accurately sampling maize's belowground microbial communities is important for identifying and characterizing these functions. Here, we describe a protocol to sample the maize rhizosphere (including the rhizoplane and endorhizosphere) and root zone (still influential but further from the root) in a form suitable for downstream analyses like culturing and DNA extractions. Although this protocol is written with <i>Zea mays</i> as the focus, these methods can generally be applied to any plant with similar fibrous root systems.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108580"},"PeriodicalIF":0.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Manipulating the Maize (Zea mays) Microbiome. 操纵玉米（Zea mays）微生物组。
Cold Spring Harbor protocols Pub Date : 2025-10-01 DOI: 10.1101/pdb.prot108584
Sierra S Raglin, Alonso Favela, Daniel Laspisa, Jason G Wallace
{"title":"Manipulating the Maize (<i>Zea mays</i>) Microbiome.","authors":"Sierra S Raglin, Alonso Favela, Daniel Laspisa, Jason G Wallace","doi":"10.1101/pdb.prot108584","DOIUrl":"10.1101/pdb.prot108584","url":null,"abstract":"<p><p>Maize (<i>Zea mays</i>) is a multifaceted cereal grass used globally for nutrition, animal feed, food processing, and biofuels, and a model system in genetics research. Studying the maize microbiome sometimes requires its manipulation to identify the contributions of specific taxa and ecological traits (i.e., diversity, richness, network structure) to maize growth and physiology. Due to regulatory constraints on applying engineered microorganisms in field settings, greenhouse-based experimentation is often the first step for understanding the contribution of root-associated microbiota-whether natural or engineered-to plant phenotypes. In this protocol, we describe methods to inoculate maize with a specific microbiome as a tool for understanding the microbiota's influence on its host plant. The protocol involves removal of the native seed microbiome followed by inoculation of new microorganisms; separate protocols are provided for inoculations from pure culture, from soil slurry, or by mixing in live soil. These protocols cover the most common methods for manipulating the maize microbiome in soil-grown plants in the greenhouse. The methods outlined will ultimately result in rhizosphere microbial assemblages with varying degrees of microbial diversity, ranging from low diversity (individual strain and synthetic community [SynCom] inoculation) to high diversity (percent live inoculation), with the slurry inoculation method representing an \"intermediate diversity\" treatment.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108584"},"PeriodicalIF":0.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Use of Maize (Zea mays L.) Mutator Transposon-Induced Mutants of the BonnMu Resource for Forward and Reverse Genetics Studies. 利用波恩姆资源的玉米（Zea mays L.）突变体转座子诱导突变体进行正向和反向遗传学研究。
Cold Spring Harbor protocols Pub Date : 2025-09-02 DOI: 10.1101/pdb.prot108587
Yan Naing Win, Martin Pöschel, Tyll Stöcker, Xuelian Du, Alina Klaus, Ben Wilhelm Braun, Linnéa Lukas, Alexa Brox, Heiko Schoof, Frank Hochholdinger, Caroline Marcon
{"title":"Use of Maize (<i>Zea mays</i> L.) Mutator Transposon-Induced Mutants of the <i>BonnMu</i> Resource for Forward and Reverse Genetics Studies.","authors":"Yan Naing Win, Martin Pöschel, Tyll Stöcker, Xuelian Du, Alina Klaus, Ben Wilhelm Braun, Linnéa Lukas, Alexa Brox, Heiko Schoof, Frank Hochholdinger, Caroline Marcon","doi":"10.1101/pdb.prot108587","DOIUrl":"10.1101/pdb.prot108587","url":null,"abstract":"<p><p>The <i>BonnMu</i> resource represents a tagged collection of maize (<i>Zea mays</i> L.) <i>Mutator</i> (<i>Mu</i>) transposon-induced mutants, designed for functional genomics studies. Here, we describe the use of the <i>BonnMu</i> collection for identifying and characterizing mutations. Specifically, we describe workflows for use in both reverse and forward genetics strategies in maize. For reverse genetics, users first acquire a <i>BonnMu</i> F<sub>2</sub> stock of interest based on data accessible at the Maize Genetics and Genomics Database (MaizeGDB). We provide details here for their subsequent propagation and for the confirmation of <i>Mu</i> insertions by genotyping via PCR, with the ultimate goal of establishing genotype-phenotype relationships of interest. For forward genetics studies, we describe a workflow that involves a combined approach of Mutant-Seq (Mu-Seq) and bulked segregant RNA-seq (BSR-Seq), to identify the causal gene underlying a mutant phenotype of interest.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108587"},"PeriodicalIF":0.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142281506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Root Anatomical Imaging and Phenotyping in Maize. 玉米根部解剖成像和表型分析
Cold Spring Harbor protocols Pub Date : 2025-09-02 DOI: 10.1101/pdb.top108454
Jagdeep Singh Sidhu, Hannah M Schneider
{"title":"Root Anatomical Imaging and Phenotyping in Maize.","authors":"Jagdeep Singh Sidhu, Hannah M Schneider","doi":"10.1101/pdb.top108454","DOIUrl":"10.1101/pdb.top108454","url":null,"abstract":"<p><p>Root anatomy plays a crucial role in regulating essential processes such as the absorption and movement of water and nutrients in plants. Root anatomy also impacts the energy costs of building and sustaining root tissues, tissue mechanics, and interactions with other organisms. Although several studies in maize have confirmed the functional utility of numerous root anatomical traits, such as that of cortical cell size and number for stress adaptation, there have been significant obstacles in measuring and analyzing root anatomical characteristics. This has resulted in gaps in our understanding of the genetic control and range of phenotypic variations among different cultivars, and how this diversity relates to overall fitness. Here, we review root anatomical phenotypes in maize and their function in stress adaptation, and briefly discuss phenotyping methods available for root anatomy. We further introduce a simple and accessible phenotyping approach that enables a comprehensive investigation of maize root anatomy. Detailed characterization of root traits and the implementation of robust methods for root anatomical phenotyping could have wide-ranging benefits across various areas of plant science, from fundamental research to enhancing crop breeding efforts.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.top108454"},"PeriodicalIF":0.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142105085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Navigating the Maze of Maize Genomics: The Impact of Transposable Elements and Tandem Repeats. 玉米基因组学的迷宫导航：可转座元件和串联重复的影响。
Cold Spring Harbor protocols Pub Date : 2025-09-02 DOI: 10.1101/pdb.top108441
Pedro Heringer, Christopher W Benson, Shujun Ou
{"title":"Navigating the Maze of Maize Genomics: The Impact of Transposable Elements and Tandem Repeats.","authors":"Pedro Heringer, Christopher W Benson, Shujun Ou","doi":"10.1101/pdb.top108441","DOIUrl":"10.1101/pdb.top108441","url":null,"abstract":"<p><p>Transposable elements (TEs) are abundant and ubiquitous components of eukaryotic genomes. Since TEs were first discovered in maize (<i>Zea mays</i>) by Barbara McClintock in the late 1940s, these elements have been shown to be important agents in shaping genome structure and evolution. Today, maize continues to be an important model organism for molecular and quantitative genetics, and represents a particularly useful system for the study of the interplay between TEs and host genomes. While TEs constitute a significant part of the maize genome and are important drivers of genome evolution, their annotation remains a complex and challenging task. Here, we discuss genome annotation of TEs and other repetitive sequences in maize genomes. We briefly review current knowledge on the overall landscape of TE and non-TE repeats in maize, and discuss how these sequences may impact genome structure, and the genotype and phenotype within species. We also provide a summary of the main tools used to find TE polymorphisms, and briefly introduce four different bioinformatic approaches for TE and tandem repeat annotation, explaining how they can be best used by maize researchers.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.top108441"},"PeriodicalIF":0.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
BonnMu: A Resource for Functional Genomics in Maize (Zea mays L.). BonnMu：玉米功能基因组学资源。
Cold Spring Harbor protocols Pub Date : 2025-09-02 DOI: 10.1101/pdb.top108465
Caroline Marcon, Yan Naing Win, Xuelian Du, Frank Hochholdinger
{"title":"<i>BonnMu</i>: A Resource for Functional Genomics in Maize (<i>Zea mays</i> L.).","authors":"Caroline Marcon, Yan Naing Win, Xuelian Du, Frank Hochholdinger","doi":"10.1101/pdb.top108465","DOIUrl":"10.1101/pdb.top108465","url":null,"abstract":"<p><p>The <i>BonnMu</i> resource is a public transposon-tagged population designed for reverse and forward genetics studies in maize (<i>Zea mays</i> L.). The resource was created by crossing an active <i>Mutator</i> (<i>Mu</i>) transposon line into different inbred lines to induce insertional mutations. The resulting F<sub>1</sub> generation was self-pollinated to generate segregating <i>BonnMu</i> F<sub>2</sub> stocks. The <i>Mu</i>-tagged <i>BonnMu</i> F<sub>2</sub> stocks have insertions in 83% of all annotated maize gene models, and <i>Mu</i> insertion positions and photos of the seedling phenotypes of the segregating <i>BonnMu</i> F<sub>2</sub> stocks are deposited in the Maize Genetics and Genomics Database (MaizeGDB), with seeds available to the community. Here, we discuss the creation, expansion, and application of the <i>BonnMu</i> resource for identifying and characterizing mutations induced by <i>Mu</i> transposons, which represents a useful tool for functional genomics studies in maize.</p>","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.top108465"},"PeriodicalIF":0.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142281497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术官方微信