Cold Spring Harbor protocols最新文献_第2页

Fresh Tissue Scanning Electron Microscopy (SEM) of Maize Meristems. 玉米分生组织的新鲜组织扫描电镜（SEM）。

Cold Spring Harbor protocols Pub Date : 2026-09-10 DOI: 10.1101/pdb.prot108748

Comfort Bonney Arku, Madelaine Bartlett, Annis E Richardson

{"title":"Fresh Tissue Scanning Electron Microscopy (SEM) of Maize Meristems.","authors":"Comfort Bonney Arku, Madelaine Bartlett, Annis E Richardson","doi":"10.1101/pdb.prot108748","DOIUrl":"https://doi.org/10.1101/pdb.prot108748","url":null,"abstract":"In plants, final organ shape and position influence function and whole plant productivity. In Zea mays (maize), leaf, ear, and tassel morphology are all key agronomic features influencing yield. These aerial structures originate from stem cell populations within meristems. Understanding how meristems are regulated and how stem cells differentiate over developmental time to form mature leaves, ears, and tassels is important for identifying novel routes for maize improvement. High-resolution imaging of meristem morphology is a key component of developmental studies. Scanning electron microscopy (SEM) is widely used to visualize meristem topology; however, conventional SEM preparation requires fixation, dehydration, drying, and conductive coating. These steps are time-consuming, technically demanding, and can introduce damage. Here, we present a rapid protocol for imaging freshly dissected meristems from maize using a benchtop scanning electron microscope. Fresh tissues are mounted directly onto conductive adhesive and imaged under high vacuum at low accelerating voltage, enabling high-quality micrographs to be captured within minutes of dissection. Although dehydration and tissue collapse can occur under vacuum, rapid sample handling and image acquisition minimize these effects and produce images comparable to those obtained from conventionally prepared specimens. This streamlined workflow substantially reduces preparation time, lowers material requirements, and facilitates medium-throughput morphological analysis. The method provides a practical and reproducible approach for rapid developmental phenotyping and is readily adaptable to other plant species and other tissues.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148929068","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

Maize Developmental Biology: Fundamental Discoveries Unlocking Innovation. 玉米发育生物学：开启创新的基本发现。

Cold Spring Harbor protocols Pub Date : 2026-09-10 DOI: 10.1101/pdb.top108451

Madelaine Bartlett, Samuel Leiboff, Annis E Richardson

{"title":"Maize Developmental Biology: Fundamental Discoveries Unlocking Innovation.","authors":"Madelaine Bartlett, Samuel Leiboff, Annis E Richardson","doi":"10.1101/pdb.top108451","DOIUrl":"https://doi.org/10.1101/pdb.top108451","url":null,"abstract":"Maize (Zea mays) is a cornerstone of agriculture and global genetics research. Every year more than 200 million hectares of maize are grown worldwide for human and animal consumption, and biofuel and energy production. Maize has also been a key research model organism since the 1800s, and over 150 years of research has led to many fundamental discoveries in genetics and developmental biology. These findings include \"jumping genes\" (transposons) and the first homeobox gene in plants, KNOTTED1, whose discovery overturned the hypothesis that homeobox genes were unique to animals. Research in maize has not only deepened our fundamental understanding of the world around us but has also driven crop improvements. Maize yield and resilience are intimately linked with plant morphology. Developmental biology aims to understand how morphology arises through the coordinated action of gene expression, hormones, cell behaviors, and biophysics across space and time. This review delves into the foundations of developmental analyses, spanning three components: morphology, time, and space. We also discuss the challenges inherent to maize developmental research, such as the inaccessibility of meristems and developing organs, and introduce techniques that address these challenges.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148929089","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

Imaging Mature Maize Morphology. 成熟玉米形态学成像。

Cold Spring Harbor protocols Pub Date : 2026-09-10 DOI: 10.1101/pdb.prot108746

Samuel Leiboff, Madelaine Bartlett, Annis E Richardson

{"title":"Imaging Mature Maize Morphology.","authors":"Samuel Leiboff, Madelaine Bartlett, Annis E Richardson","doi":"10.1101/pdb.prot108746","DOIUrl":"https://doi.org/10.1101/pdb.prot108746","url":null,"abstract":"Zea mays (maize) is a critical global crop, generating more than 1 billion metric tons of grain annually. Plant morphology is tightly associated with final yield and is determined by the process of development. Accurate assessment and recording of mature plant morphology is essential for linking genotype to phenotype and for assessing environmental influences on plant development and yield. In maize, imaging of fully emerged aerial organs provides an accessible and informative developmental end point for comparative phenotypic analyses. Here, we provide a protocol for capturing high-quality images of mature maize plants and detached leaf blades, suitable for publication and downstream quantitative trait extraction. We emphasize standardized imaging conditions, including high-contrast backgrounds, diffuse lighting, fixed camera positioning, and consistent scale calibration, to minimize technical variation and to facilitate automated image processing. Guidance is provided for both laboratory- and field-based imaging setups and uses widely available equipment. Images generated using this protocol can be analyzed using platforms such as FIJI to extract morphometric traits, including length, width, and outline-based shape descriptors. By prioritizing standardization at the point of acquisition, this protocol supports reproducible, scalable phenotyping of mature maize morphology for developmental studies in maize.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148929007","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

Dissecting Maize Aerial Meristems. 解剖玉米地上分生组织。

Cold Spring Harbor protocols Pub Date : 2026-09-10 DOI: 10.1101/pdb.prot108747

Madelaine Bartlett, Annis E Richardson

{"title":"Dissecting Maize Aerial Meristems.","authors":"Madelaine Bartlett, Annis E Richardson","doi":"10.1101/pdb.prot108747","DOIUrl":"https://doi.org/10.1101/pdb.prot108747","url":null,"abstract":"The plant kingdom displays a wide array of shapes, and this morphology is tightly linked to function and productivity. For example, leaf size, shape, and arrangement around the stem define canopy architecture, influencing light interception and photosynthetic capacity. Understanding how final morphology is determined is, therefore, not only important for our basic understanding of various plant species, but also an essential tool in the development of new crop varieties. All aerial organs in flowering plants arise on the flanks of meristems throughout development. In Zea mays (maize), these meristems are deeply enclosed within successive leaf layers, making their identification and isolation technically challenging. Successful dissection requires accurate staging, recognition of anatomical landmarks, and careful tissue handling to avoid damage or desiccation. These challenges can present a significant barrier to researchers attempting maize developmental biology studies. Here, we provide a practical, step-by-step guide for identifying and dissecting vegetative shoot apical, tassel, and ear meristems. The protocol integrates external morphological cues, nodal position, stem texture, and diagnostic cross-sectional features to distinguish cuts made above, through, or below the meristem. Detailed strategies are described to sequentially remove enclosing leaf primordia, while preserving meristem integrity. By formalizing techniques often transmitted informally within laboratories, this protocol lowers the barrier to entry for maize meristem research, supporting downstream applications including imaging, gene expression analysis, and developmental phenotyping.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148929093","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

Sample Preparation for Quantitative Proteome and Phosphoproteome Profiling of Maize Tissues. 玉米组织定量蛋白质组和磷酸化蛋白质组分析的样品制备。

Cold Spring Harbor protocols Pub Date : 2026-08-25 DOI: 10.1101/pdb.prot108733

Shikha Malik, Gaoyuan Song, Christian Montes, Justin W Walley

{"title":"Sample Preparation for Quantitative Proteome and Phosphoproteome Profiling of Maize Tissues.","authors":"Shikha Malik, Gaoyuan Song, Christian Montes, Justin W Walley","doi":"10.1101/pdb.prot108733","DOIUrl":"10.1101/pdb.prot108733","url":null,"abstract":"Zea mays (maize) is a globally important cereal crop and a key system for studying plant development and stress responses. Proteome profiling and phosphoproteome profiling provide direct, quantitative readouts of protein abundance and phosphorylation states, which offer insights into aspects of regulation and cellular function that transcript-level measurements alone cannot provide. Robust and reproducible methods are essential for generating accurate and biologically relevant data in proteomics studies. The complexity of plant tissues, however, poses challenges for developing reliable sample preparation workflows. Here, we describe a detailed sample preparation protocol for quantitative proteome and phosphoproteome profiling in maize. The protocol encompasses protein extraction, filter-aided sample preparation (FASP), peptide desalting, tandem mass tag (TMT)-based labeling for quantitative multiplexing, and complementary TiO2 and Fe-NTA enrichment steps, yielding peptides suitable for analysis by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). This approach enables the quantitative profiling of protein abundance and phosphorylation dynamics in maize tissues.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108733"},"PeriodicalIF":0.0,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403830","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

Functional Genomic Analysis of Transposon Insertion Mutant Maize Plants from the UniformMu National Public Resource. UniformMu国家公共资源玉米转座子插入突变体的功能基因组分析。

Cold Spring Harbor protocols Pub Date : 2026-08-25 DOI: 10.1101/pdb.prot108688

Donald R McCarty, Karen E Koch

{"title":"Functional Genomic Analysis of Transposon Insertion Mutant Maize Plants from the UniformMu National Public Resource.","authors":"Donald R McCarty, Karen E Koch","doi":"10.1101/pdb.prot108688","DOIUrl":"10.1101/pdb.prot108688","url":null,"abstract":"The UniformMu National Public Resource is a widely used, functional genomics tool for maize, constructed by backcross introgression of active Robertson's Mutator (Mu) transposons into the W22 inbred line, creating a large, searchable collection of lines that together carry transposon insertions in thousands of maize genes. This resource provides (1) a ready supply of freely available mutant seed stocks, each linked to mapped gene sequences; (2) uniform controls in an inbred background, for precision analysis of mutant phenotypes; (3) a reliable source of heritable mutants that are consistently recovered in stated lines; and (4) stable mutant lines with no Mu activity. This low-cost resource provides a consummate experimental system for linking gene sequences with their function in a species that has long served humanity, not only as a preeminent genetic model, but also as one of the world's most productive grain crops. Here, we describe how to perform an initial, online search of insertions in the UniformMu population, request seeds, generate segregating families, PCR-genotype seedlings for Mu insertions of interest, and associate genotypes with phenotypes. Resulting analyses provide definitive, in planta evidence for genotype-phenotype relationships that either support or refute hypotheses regarding gene function.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108688"},"PeriodicalIF":0.0,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145512155","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

Emerging Trends in Mass Spectrometry-Based Quantitative Proteome and Phosphoproteome Profiling in Maize. 基于质谱的玉米定量蛋白质组和磷蛋白质组分析的新趋势。

Cold Spring Harbor protocols Pub Date : 2026-08-25 DOI: 10.1101/pdb.top108452

Shikha Malik, Justin W Walley

{"title":"Emerging Trends in Mass Spectrometry-Based Quantitative Proteome and Phosphoproteome Profiling in Maize.","authors":"Shikha Malik, Justin W Walley","doi":"10.1101/pdb.top108452","DOIUrl":"10.1101/pdb.top108452","url":null,"abstract":"Maize (Zea mays) is both an agronomically important crop and a reference model organism that has enabled the dissection of the molecular basis of plant development and environmental responses. Mass spectrometry-based proteomics provides a powerful approach to identify and quantify proteins and their post-translational modifications, facilitating the discovery of molecular mechanisms underlying complex biological processes. Unlike the study of gene expression using transcriptomics, analysis of the proteome and phosphoproteome provides direct measurement of proteins, which are responsible for driving or regulating nearly all cellular processes, thus offering a more complete picture of the cell's functional state. Over the past two decades, advancements in mass spectrometry have enabled large-scale profiling of protein abundance and phosphorylation sites in maize, improving our understanding of various biological phenomena. Here, we briefly summarize some of the major biological insights gained from maize proteome and phosphoproteome studies, and provide an overview of mass spectrometry sample preparation and acquisition/analysis workflows for the quantitative and reproducible analysis of protein abundance and phosphorylation dynamics in maize.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.top108452"},"PeriodicalIF":0.0,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403793","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

Procedures for Standardized Measurements of Core Traits in Maize Research and Breeding Programs. 玉米研究和育种计划中核心性状的标准化测量程序。

Cold Spring Harbor protocols Pub Date : 2026-08-25 DOI: 10.1101/pdb.prot108734

Dayane Cristina Lima, Natalia de Leon, Shawn M Kaeppler

{"title":"Procedures for Standardized Measurements of Core Traits in Maize Research and Breeding Programs.","authors":"Dayane Cristina Lima, Natalia de Leon, Shawn M Kaeppler","doi":"10.1101/pdb.prot108734","DOIUrl":"10.1101/pdb.prot108734","url":null,"abstract":"Maize (Zea mays L.) is a highly adaptable crop grown worldwide across diverse climates and management practices, with uses across multiple sectors. Consequently, the traits prioritized in maize research and breeding programs vary depending on the specific objectives. Core traits, however, such as flowering time, plant and ear height, and stalk and root lodging, which are important for evaluating and improving the performance and stability of maize genotypes, are routinely evaluated across breeding programs, regardless of their goals. Standardized measurement of these core traits is essential to ensure data reliability and comparability, enabling the integration of phenotypic data across different experiments. Such efforts ultimately support better decision-making and accelerate the development of improved maize genotypes. This is particularly important in public sector programs, where large-scale evaluations, critical for assessing the value of specific genotypes, are often only feasible through collaboration across programs. Here, we provide a protocol for the standardized collection of phenotypic data, specifically focusing on how to measure core traits in maize field trials. These methods promote consistency and accuracy in the evaluation of these traits, and support communication and coordination among groups in the public sector and other research settings. Further, such standardization facilitates the integration and comparison of data across programs, enabling robust longitudinal and multienvironment analyses.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.prot108734"},"PeriodicalIF":0.0,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535564","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

Standardized Trait Measurement in Maize Breeding and Genetics Research. 玉米育种与遗传研究中的标准化性状测量。

Cold Spring Harbor protocols Pub Date : 2026-08-25 DOI: 10.1101/pdb.top108453

Dayane Cristina Lima, Natalia de Leon, Shawn M Kaeppler

{"title":"Standardized Trait Measurement in Maize Breeding and Genetics Research.","authors":"Dayane Cristina Lima, Natalia de Leon, Shawn M Kaeppler","doi":"10.1101/pdb.top108453","DOIUrl":"10.1101/pdb.top108453","url":null,"abstract":"Maize (Zea mays L.) is a highly versatile crop, grown worldwide under different climatic conditions and management practices. Its wide-ranging uses across multiple sectors, including food and feed production, biofuels, and as a source of raw materials for industrial processes, make the traits of interest highly variable, depending on research and breeding goals and the needs of commercial and public end users. The phenotype observed in these contexts reflects the combined effects of the genotype, the environment, and their interaction, making multienvironment trials crucial for identifying superior cultivars and predicting their performance across diverse conditions. Accurate and consistent trait measurements and recording are therefore essential to enable meaningful comparisons and integration of data across years, locations, and studies. This is particularly important in the public sector, where such multienvironment trails are often only feasible primarily through collaborative efforts. Here, we provide a brief overview of the importance of standardized trait measurements in maize research and breeding programs, and discuss their impact on enhancing the value and usability of publicly accessible phenotyping data. We also highlight how standardization helps overcome the challenges of conducting large-scale experiments across locations and years, particularly in resource-limited public programs, where multiinstitutional coordination is essential. Together, these approaches help advance reproducibility and data sharing across maize research programs.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.top108453"},"PeriodicalIF":0.0,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535517","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

The UniformMu National Public Resource: Transposon-Induced Mutant Seeds for Functional Genomics Studies in Maize. UniformMu国家公共资源：用于功能基因组学研究的转座子诱导突变种子。

Cold Spring Harbor protocols Pub Date : 2026-08-25 DOI: 10.1101/pdb.top108483

Karen E Koch, Donald R McCarty

{"title":"The UniformMu National Public Resource: Transposon-Induced Mutant Seeds for Functional Genomics Studies in Maize.","authors":"Karen E Koch, Donald R McCarty","doi":"10.1101/pdb.top108483","DOIUrl":"10.1101/pdb.top108483","url":null,"abstract":"Geneticists frequently use loss-of-function (knockout) mutations to reveal the effects of a gene's dysfunction at the organismal level, observed as the mutant phenotype. This strategy is facilitated by creation of large, searchable collections of knockout mutants in an organism of interest. Paramount among such resources in maize is the UniformMu National Resource, a large collection of genetic stocks carrying mutations generated by insertions of Robertson's Mutator (Mu) transposons. The name UniformMu refers to the phenotypic uniformity of the W22 inbred genetic background in which Mu insertion mutants were created. This community resource continues its pivotal role in providing seeds containing beneficial knockout and knockdown mutations in targeted genes, which can be used to elucidate gene function. The resource offers an invaluable complement to other functional genomics approaches aimed at bridging the gap between genome sequences and plant performance in the field. Several key features are central to the success of the UniformMu National Public Resource. First, mapped insertions are linked to seed stocks that are readily available through the Maize Genetics and Genomics Database (MaizeGDB) and the Maize Genetics Cooperation Stock Center. Second, a uniform inbred background facilitates analysis of mutant phenotypes, by providing uniform wild-type controls. Third, mutant alleles are reliably heritable and consistently recovered in stated lines. Finally, lines are stable, with no continuing transposition of Mu insertions. The collective effort of the maize community allows UniformMu to provide readily accessible knockout and knockdown mutant seeds, as well as, ultimately, highly sought evidence for gene function in planta.","PeriodicalId":10496,"journal":{"name":"Cold Spring Harbor protocols","volume":" ","pages":"pdb.top108483"},"PeriodicalIF":0.0,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145512098","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