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Current protocols in plant biology最新文献

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Handling Fast-Flowering Mini-Maize 处理快速开花的迷你玉米
Current protocols in plant biology Pub Date : 2017-06-21 DOI: 10.1002/cppb.20051
Morgan E. McCaw, James A. Birchler
{"title":"Handling Fast-Flowering Mini-Maize","authors":"Morgan E. McCaw,&nbsp;James A. Birchler","doi":"10.1002/cppb.20051","DOIUrl":"10.1002/cppb.20051","url":null,"abstract":"<p>Maize (<i>Zea mays</i>) has a long history as a model organism for genetic analysis due to its ease of crossing, relatively large number of progeny, and ability to determine many genotypic traits through phenotypic kernel markers. Fast-Flowering Mini-Maize A and B (FFMM) are two recently developed lines of maize selected for traits that make them more conducive to research. FFMM flowers more quickly than standard maize and is much smaller; thus it requires a slightly modified protocol for care and crossing. The following protocol describes how to plant, care for, and cross FFMM in greenhouse, growth chamber, and field conditions. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"2 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"93009844","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: 3
Whole-Plant Manual and Image-Based Phenotyping in Controlled Environments 受控环境下的全植物手册和基于图像的表型分析
Current protocols in plant biology Pub Date : 2017-03-03 DOI: 10.1002/cppb.20044
Erica Agnew, Adam Bray, Eric Floro, Nate Ellis, John Gierer, César Lizárraga, Darren O'Brien, Madeline Wiechert, Todd C. Mockler, Nadia Shakoor, Christopher N. Topp
{"title":"Whole-Plant Manual and Image-Based Phenotyping in Controlled Environments","authors":"Erica Agnew,&nbsp;Adam Bray,&nbsp;Eric Floro,&nbsp;Nate Ellis,&nbsp;John Gierer,&nbsp;César Lizárraga,&nbsp;Darren O'Brien,&nbsp;Madeline Wiechert,&nbsp;Todd C. Mockler,&nbsp;Nadia Shakoor,&nbsp;Christopher N. Topp","doi":"10.1002/cppb.20044","DOIUrl":"10.1002/cppb.20044","url":null,"abstract":"<p>Phenotypic measurements and images of crops grown under controlled-environment conditions can be analyzed to compare plant growth and other phenotypes from diverse varieties. Those demonstrating the most favorable phenotypic traits can then be used for crop improvement strategies. This article details a protocol for image-based root and shoot phenotyping of plants grown in the greenhouse to compare traits among different varieties. Diverse maize lines were grown in the greenhouse in large 8-gallon treepots in a clay granule substrate. Replicates of each line were harvested at 4 weeks, 6 weeks, and 8 weeks after planting to capture developmental information. Whole-plant phenotypes include biomass accumulation, ontogeny, architecture, and photosynthetic efficiency of leaves. Image analysis was used to measure leaf surface area and tassel size and to extract shape variance information from complex 3D root architectures. Notably, this framework is extensible to any number of above- or below-ground phenotypes, both morphological and physiological. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41789827","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: 4
A Guide to Genome-Wide Association Mapping in Plants 植物全基因组关联定位指南
Current protocols in plant biology Pub Date : 2017-03-03 DOI: 10.1002/cppb.20041
Liana T. Burghardt, Nevin D. Young, Peter Tiffin
{"title":"A Guide to Genome-Wide Association Mapping in Plants","authors":"Liana T. Burghardt,&nbsp;Nevin D. Young,&nbsp;Peter Tiffin","doi":"10.1002/cppb.20041","DOIUrl":"10.1002/cppb.20041","url":null,"abstract":"<p>Genome-wide association studies (GWAS) have developed into a valuable approach for identifying the genetic basis of phenotypic variation. In this article, we provide an overview of the design, analysis, and interpretation of GWAS. First, we present results from simulations that explore key elements of experimental design as well as considerations for collecting the relevant genomic and phenotypic data. Next, we outline current statistical methods and tools used for GWA analyses and discuss the inclusion of covariates to account for population structure and the interpretation of results. Given that many false positive associations will occur in any GWA analysis, we highlight strategies for prioritizing GWA candidates for further statistical and empirical validation. While focused on plants, the material we cover is also applicable to other systems. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46592828","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: 67
Characterization of Plant Small RNAs by Next Generation Sequencing 植物小rna的下一代测序研究
Current protocols in plant biology Pub Date : 2017-03-03 DOI: 10.1002/cppb.20043
Sandra M. Mathioni, Atul Kakrana, Blake C. Meyers
{"title":"Characterization of Plant Small RNAs by Next Generation Sequencing","authors":"Sandra M. Mathioni,&nbsp;Atul Kakrana,&nbsp;Blake C. Meyers","doi":"10.1002/cppb.20043","DOIUrl":"10.1002/cppb.20043","url":null,"abstract":"<p>Plant small RNAs are ∼20 to 24 nucleotide noncoding RNAs that typically have repressive regulatory roles in gene expression, functioning at the transcriptional or post-transcriptional level. This influence on regulation of developmental and physiological processes has direct effects on phenotype. High-throughput sequencing technologies have enabled the sequencing of millions of small RNAs. Along with decreased sequencing costs, recent improvements in small RNA library construction have facilitated the ability to use minimal amounts of input RNA for analysis. This unit describes steps to isolate total RNA from limited amounts of plant tissue to construct small RNA libraries and perform small RNA data processing. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42502566","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: 28
Genotyping-by-Sequencing Genotyping-by-Sequencing
Current protocols in plant biology Pub Date : 2017-03-03 DOI: 10.1002/cppb.20042
Jason G. Wallace, Sharon E. Mitchell
{"title":"Genotyping-by-Sequencing","authors":"Jason G. Wallace,&nbsp;Sharon E. Mitchell","doi":"10.1002/cppb.20042","DOIUrl":"10.1002/cppb.20042","url":null,"abstract":"<p>Genotyping-by-sequencing (GBS) refers to a suite of related methods that obtain genotype data from samples by using restriction enzyme digestion followed by high-throughput sequencing. GBS is a refinement of restriction site–associated DNA sequencing (RADseq) methods, with a goal of being able to perform library preparations quickly, cost-effectively, and in a high-throughput manner. This protocol contains the steps necessary to go from purified DNA to Illumina-ready libraries. It also covers the considerations that go into planning a GBS experiment. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42317874","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: 44
Metaphase Chromosome Preparation from Soybean (Glycine max) Root Tips 大豆(甘氨酸)根尖中期染色体的制备
Current protocols in plant biology Pub Date : 2017-03-03 DOI: 10.1002/cppb.20046
Seth D. Findley, James A. Birchler, Gary Stacey
{"title":"Metaphase Chromosome Preparation from Soybean (Glycine max) Root Tips","authors":"Seth D. Findley,&nbsp;James A. Birchler,&nbsp;Gary Stacey","doi":"10.1002/cppb.20046","DOIUrl":"10.1002/cppb.20046","url":null,"abstract":"<p>This unit presents a highly reliable protocol to produce and screen metaphase chromosome spreads from root tip cell suspensions of soybean (<i>Glycine max</i>), or other legumes. The procedures represent soybean-optimized versions of protocols developed for maize. The use of pressurized nitrous oxide to reliably generate metaphase-arrested chromosomes is crucial to overcoming one of the challenges of working with tiny and numerous soybean chromosomes. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20046","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41437246","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: 3
Fluorescence In Situ Hybridization for Glycine max Metaphase Chromosomes 甘氨酸max中期染色体的荧光原位杂交
Current protocols in plant biology Pub Date : 2017-03-03 DOI: 10.1002/cppb.20045
Seth D. Findley, James A. Birchler, Gary Stacey
{"title":"Fluorescence In Situ Hybridization for Glycine max Metaphase Chromosomes","authors":"Seth D. Findley,&nbsp;James A. Birchler,&nbsp;Gary Stacey","doi":"10.1002/cppb.20045","DOIUrl":"10.1002/cppb.20045","url":null,"abstract":"<p>This article presents protocols for fluorescence in situ hybridization (FISH) in the cultivated soybean, <i>Glycine max</i>. The protocols represent soybean-optimized versions developed for maize. We describe the use of two different probes types: genomic-repeat-based fluorescently-tagged oligonucleotides and bacterial artificial chromosomes (BACs). The two probe types can be used either individually or together, depending on the experimental questions. The article also includes starting points for executing FISH in additional legume species. © 2017 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41371953","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: 3
Pachytene Chromosome Preparation in Populus deltoides Marsh 沼泽杨粗线染色体的制备
Current protocols in plant biology Pub Date : 2016-12-01 DOI: 10.1002/cppb.20036
Haoyang Xin, Yue Lan, Jisen Shi, Yan Ma, Mengli Xi
{"title":"Pachytene Chromosome Preparation in Populus deltoides Marsh","authors":"Haoyang Xin,&nbsp;Yue Lan,&nbsp;Jisen Shi,&nbsp;Yan Ma,&nbsp;Mengli Xi","doi":"10.1002/cppb.20036","DOIUrl":"10.1002/cppb.20036","url":null,"abstract":"<p>A technique that produces large numbers of good quality pachytene chromosome preparations has been developed for <i>Populus</i>. Anthers at the pachytene stage of meiosis are used as materials. There are two main modifications in our method relative to the traditional squashing method that address the challenges the thick cytoplasm observed during the pachytene phase of meiosis presents. One is the temperature during squashing, i.e., the slide is placed on a 52°C heater for squashing. The other is the removal of the cover slip using 45% acetic acid. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"1 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50903594","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: 2
Mass Spectrometry Imaging of Metabolites in Barley Grain Tissues 大麦籽粒组织代谢产物的质谱成像研究
Current protocols in plant biology Pub Date : 2016-12-01 DOI: 10.1002/cppb.20037
Manuela Peukert, Wai Li Lim, Udo Seiffert, Andrea Matros
{"title":"Mass Spectrometry Imaging of Metabolites in Barley Grain Tissues","authors":"Manuela Peukert,&nbsp;Wai Li Lim,&nbsp;Udo Seiffert,&nbsp;Andrea Matros","doi":"10.1002/cppb.20037","DOIUrl":"10.1002/cppb.20037","url":null,"abstract":"<p>Higher plants are composed of a multitude of tissues with particular functions, reflected by distinct profiles of transcripts, proteins, and metabolites. Although the rapid development of “omics” technologies has advanced plant science tremendously within recent years, analysis is frequently performed on whole organ or whole plant extracts, causing the loss of spatial information. Mass spectrometry–based imaging (MSI) approaches have become a powerful tool to decipher spatially resolved molecular information. Matrix-assisted laser desorption/ionization (MALDI) is the most widespread ionization method utilized for MSI and has recently been applied to plant science. A range of different plant organs and tissues has been successfully analyzed by MSI, and patterns of various classes of metabolites from primary and secondary metabolism have been obtained. This protocol describes a method for analysis of spatial metabolite distributions in cryosections of developing barley grains. Detailed procedures for sample preparation, mass spectrometry measurement, and data analysis are provided. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"1 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50903263","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: 13
Live-Cell Imaging of Meiotic Spindle and Chromosome Dynamics in Maize (Zea mays) 玉米减数分裂纺锤体活细胞成像及染色体动力学
Current protocols in plant biology Pub Date : 2016-12-01 DOI: 10.1002/cppb.20035
Natalie J. Nannas, R. Kelly Dawe
{"title":"Live-Cell Imaging of Meiotic Spindle and Chromosome Dynamics in Maize (Zea mays)","authors":"Natalie J. Nannas,&nbsp;R. Kelly Dawe","doi":"10.1002/cppb.20035","DOIUrl":"10.1002/cppb.20035","url":null,"abstract":"<p>Live-cell imaging is a powerful tool that allows investigators to directly observe the dynamics of cellular processes. Live imaging has proven particularly useful in studying mitotic and meiotic chromosome segregation, where the assembly of spindles and movement of chromosomes can be quantified in ways not possible with fixed cells. This protocol describes how to image live meiosis in the agriculturally important plant, maize. The creation of fluorescently tagged tubulin allows visualization of maize spindles, and nucleic acid dyestain chromosomes. This protocol describes all steps required for live imaging, including how to grow plants, screen for relevant genotypes, harvest meiotic cells, and collect live movies of meiosis. While this protocol was developed for imaging fluorescently tagged tubulin, it can be easily modified to observe the meiotic dynamics of any fluorescently labeled protein of interest. © 2016 by John Wiley &amp; Sons, Inc.</p>","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"1 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50903544","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: 4
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