Current protocols in plant biology最新文献_第2页

CRISPR/Cas9-Based Genome Editing Using Rice Zygotes 基于CRISPR/ cas9的水稻受精卵基因组编辑

Current protocols in plant biology Pub Date : 2020-06-09 DOI: 10.1002/cppb.20111

Erika Toda, Takashi Okamoto

{"title":"CRISPR/Cas9-Based Genome Editing Using Rice Zygotes","authors":"Erika Toda, Takashi Okamoto","doi":"10.1002/cppb.20111","DOIUrl":"10.1002/cppb.20111","url":null,"abstract":"Genome-editing technology involving the targeted mutagenesis of plants using programmable nucleases has been developing rapidly and has enormous potential in next-generation plant breeding. Its application has been hindered in many cases, however, due to technical hurdles, such as the low rate of macromolecule delivery into plant cells and tissues or difficulties in plant transformation and regeneration. Here, a protocol for CRISPR/Cas9-based genome editing using rice zygotes is described. The genome-editing system is constructed via polyethylene glycol/calcium-mediated transfection with CRISPR/Cas9 components in rice zygotes, which are produced by in vitro fertilization of isolated rice gametes. Plasmid DNA harboring a CRISPR/Cas9 expression cassette or preassembled Cas9 protein–guide RNA ribonucleoproteins is transfected into zygotes, resulting in the regeneration of plants with a high frequency of the targeted mutation, which is either mono-allelic or bi-allelic, in the range of about 4% to 64%. Application of the present method has the potential to advance the molecular breeding of other crop species as well as rice. © 2020 Wiley Periodicals LLC.","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38024889","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: 8

Use of CRISPR/Cas9 for Targeted Mutagenesis in Sorghum CRISPR/Cas9在高粱靶向诱变中的应用

Current protocols in plant biology Pub Date : 2020-06-05 DOI: 10.1002/cppb.20112

Si Nian Char, Hyeyoung Lee, Bing Yang

{"title":"Use of CRISPR/Cas9 for Targeted Mutagenesis in Sorghum","authors":"Si Nian Char, Hyeyoung Lee, Bing Yang","doi":"10.1002/cppb.20112","DOIUrl":"10.1002/cppb.20112","url":null,"abstract":"Sorghum (Sorghum bicolor) fulfills the demand for bioenergy resources and also provides substantial diet calories to the world's population. Therefore, many biological studies use sorghum as a research model for improvement of the domesticated food and bioenergy crops. Furthermore, leveraging genome editing systems in a plethora of grass plant species has been extensively studied with no exception in sorghum. However, a protocol that details the genome editing strategies using CRISPR/Cas9 and that combines an efficient tissue culture and transformation platform in sorghum based on Agrobacterium-mediated DNA transfer has yet to be reported. This protocol outlines the steps and workflow from design of sorghum CRISPR target sites using BTx623 as a reference genome, construction of sorghum CRISPR/Cas9 plasmids, tissue culture, to Agrobacterium-mediated transformation followed by genotyping of CRISPR/Cas9 induced mutants. © 2020 Wiley Periodicals LLC.Basic Protocol 1: Construction of CRISPR/Cas9 expression vector to analysis of CRISPR-edited plantsBasic Protocol 2: Stable transformation of sorghumSupport Protocol: Management of sorghum plants in a greenhouse","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38017165","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: 9

Liquid Chromatography–Mass Spectrometry (LC-MS)-Based Analysis for Lipophilic Compound Profiling in Plants 基于液相色谱-质谱(LC-MS)的植物亲脂性化合物谱分析

Current protocols in plant biology Pub Date : 2020-04-28 DOI: 10.1002/cppb.20109

Taly Lapidot-Cohen, Leah Rosental, Yariv Brotman

{"title":"Liquid Chromatography–Mass Spectrometry (LC-MS)-Based Analysis for Lipophilic Compound Profiling in Plants","authors":"Taly Lapidot-Cohen, Leah Rosental, Yariv Brotman","doi":"10.1002/cppb.20109","DOIUrl":"10.1002/cppb.20109","url":null,"abstract":"Lipids are fascinating due to their chemical diversity, which is especially vast in the plant kingdom thanks to the high plasticity of the plant biosynthetic machinery. Lipidomic studies aim to simultaneously analyze a large number of lipid compounds of diverse classes in a given sample. The method presented here uses liquid chromatography–mass spectrometry (LC-MS)-based lipidomic profiling in a relatively fast, robust, and high-throughput manner for high-coverage quantification and annotation of lipophilic compounds. Protocols cover sample preparation, LC-MS-based measurement, and data extraction and annotation. An extensive lipid library for triacylglycerols, galactolipids, and phospholipids is provided. The extended profiling described here could be used in a range of applications and is suitable for integration with other omic datasets. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Sample preparation and metabolite extractionBasic Protocol 2: Liquid chromatography–mass spectrometry (LC-MS) analysisBasic Protocol 3: Data extraction, annotation, and quantification","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37879865","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: 10

Analysis of Tomato Post-Harvest Properties: Fruit Color, Shelf Life, and Fungal Susceptibility 番茄采后特性分析:果实颜色、保质期和真菌敏感性

Current protocols in plant biology Pub Date : 2020-04-20 DOI: 10.1002/cppb.20108

Vera Thole, Philippe Vain, Ray-Yu Yang, Juliana Almeida Barros da Silva, Eugenia M. A. Enfissi, Marilise Nogueira, Elliott J. Price, Saleh Alseekh, Alisdair R. Fernie, Paul D. Fraser, Peter Hanson, Cathie Martin

{"title":"Analysis of Tomato Post-Harvest Properties: Fruit Color, Shelf Life, and Fungal Susceptibility","authors":"Vera Thole, Philippe Vain, Ray-Yu Yang, Juliana Almeida Barros da Silva, Eugenia M. A. Enfissi, Marilise Nogueira, Elliott J. Price, Saleh Alseekh, Alisdair R. Fernie, Paul D. Fraser, Peter Hanson, Cathie Martin","doi":"10.1002/cppb.20108","DOIUrl":"10.1002/cppb.20108","url":null,"abstract":"A wide variety of fresh market and processing tomatoes (Solanum lycopersicum) is grown and consumed worldwide. Post-harvest losses are a major contributing factor to losses in crop productivity and can account for up to 50% of the harvest. To select and breed elite tomato varieties, it is important to characterize fruit quality and evaluate the post-harvest properties of tomato fruits. This includes the analysis of shelf life (the period during which a fruit remains suitable for consumption without qualitative deterioration), color, and pathogen susceptibility. Tomato shelf life depends upon the rate of fruit softening which accompanies fruit ripening and exacerbates damage during transport and handling. Furthermore, the susceptibility of tomatoes to fruit pathogens is also often linked to fruit ripening, especially for necrotrophic fungi such as Botrytis cinerea, also known as gray mold. The methods described here are critical for determining fruit quality and fungal susceptibility during storage. © 2020 The Authors.Basic Protocol 1: Fruit color as a determinant of fruit qualityBasic Protocol 2: Shelf life test of tomato fruitsBasic Protocol 3: Botrytis cinerea pathogen test of tomato fruitsSupport Protocol: Preparation of Botrytis spore inoculum","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20108","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37851989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 18

Measuring the Hydraulic Conductivity of Grass Root Systems 测量根系的水力传导性

Current protocols in plant biology Pub Date : 2020-04-20 DOI: 10.1002/cppb.20110

Atara Gal, Elisha Hendel, Zvi Peleg, Nimrod Schwartz, Nir Sade

引用次数: 2

Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for the Analysis of Protein Oligomers in Plants 蓝色原生聚丙烯酰胺凝胶电泳(BN-PAGE)分析植物蛋白质低聚物

Current protocols in plant biology Pub Date : 2020-04-06 DOI: 10.1002/cppb.20107

Pratchaya Pramoj Na Ayutthaya, Derek Lundberg, Detlef Weigel, Lei Li

引用次数: 11

Supervised Learning of Gene Regulatory Networks 基因调控网络的监督学习

Current protocols in plant biology Pub Date : 2020-03-24 DOI: 10.1002/cppb.20106

Zahra Razaghi-Moghadam, Zoran Nikoloski

{"title":"Supervised Learning of Gene Regulatory Networks","authors":"Zahra Razaghi-Moghadam, Zoran Nikoloski","doi":"10.1002/cppb.20106","DOIUrl":"10.1002/cppb.20106","url":null,"abstract":"Identifying the entirety of gene regulatory interactions in a biological system offers the possibility to determine the key molecular factors that affect important traits on the level of cells, tissues, and whole organisms. Despite the development of experimental approaches and technologies for identification of direct binding of transcription factors (TFs) to promoter regions of downstream target genes, computational approaches that utilize large compendia of transcriptomics data are still the predominant methods used to predict direct downstream targets of TFs, and thus reconstruct genome-wide gene-regulatory networks (GRNs). These approaches can broadly be categorized into unsupervised and supervised, based on whether data about known, experimentally verified gene-regulatory interactions are used in the process of reconstructing the underlying GRN. Here, we first describe the generic steps of supervised approaches for GRN reconstruction, since they have been recently shown to result in improved accuracy of the resulting networks? We also illustrate how they can be used with data from model organisms to obtain more accurate prediction of gene regulatory interactions. © 2020 The Authors.Basic Protocol 1: Construction of features used in supervised learning of gene regulatory interactionsBasic Protocol 2: Learning the non-interacting TF-gene pairsBasic Protocol 3: Learning a classifier for gene regulatory interactions","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20106","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37767287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Agrobacterium tumefaciens–Mediated Transformation of Three Milkweed Species (Asclepias hallii, A. syriaca, and A. tuberosa: Apocynaceae) 农杆菌介导的三种乳草(夹竹桃科)的转化

Current protocols in plant biology Pub Date : 2020-03-09 DOI: 10.1002/cppb.20105

Patricia Keen, Amy Picard Hastings, Anurag A. Agrawal, Joyce Van Eck

{"title":"Agrobacterium tumefaciens–Mediated Transformation of Three Milkweed Species (Asclepias hallii, A. syriaca, and A. tuberosa: Apocynaceae)","authors":"Patricia Keen, Amy Picard Hastings, Anurag A. Agrawal, Joyce Van Eck","doi":"10.1002/cppb.20105","DOIUrl":"10.1002/cppb.20105","url":null,"abstract":"Milkweeds have ecological significance for insect herbivores that rely on them as hosts for either part of or the entirety of their life cycles. Interesting interactions, some of which are not completely understood, have evolved over time. To develop these species as models to elucidate the interplay with insect herbivores, we established Agrobacterium tumefaciens–mediated transformation approaches for Asclepias hallii (Hall's milkweed), A. syriaca (common milkweed), and A. tuberosa (butterflyweed). The method is based on infection of stem internodal explants, which were more amenable to transformation than leaf explants. We found that addition of freshly prepared dithiothreitol was critical to prevent browning of stem explants. Depending on the species, the time from infection to the regeneration of transgenic lines ranges from 2 to 4 months. Transformation efficiency for A. hallii was 9%, whereas efficiencies for A. syriaca and A. tuberosa were 6% and 13%, respectively. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Agrobacterium tumefaciens–mediated transformation of Asclepias internodal stem explantsBasic Protocol 2: Preparation of Agrobacterium glycerol stocks containing gene constructs","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37719509","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: 1

Nano and Micro Unmanned Aerial Vehicles (UAVs): A New Grand Challenge for Precision Agriculture? 纳米和微型无人机:精准农业的新挑战?

Current protocols in plant biology Pub Date : 2020-02-19 DOI: 10.1002/cppb.20103

Jorge Gago, Joan Estrany, Lyndon Estes, Alisdair R. Fernie, Bartomeu Alorda, Yariv Brotman, Jaume Flexas, José Mariano Escalona, Hipólito Medrano

{"title":"Nano and Micro Unmanned Aerial Vehicles (UAVs): A New Grand Challenge for Precision Agriculture?","authors":"Jorge Gago, Joan Estrany, Lyndon Estes, Alisdair R. Fernie, Bartomeu Alorda, Yariv Brotman, Jaume Flexas, José Mariano Escalona, Hipólito Medrano","doi":"10.1002/cppb.20103","DOIUrl":"10.1002/cppb.20103","url":null,"abstract":"By collecting data at spatial and temporal scales that are inaccessible to satellite and field observation, unmanned aerial vehicles (UAVs) are revolutionizing a number of scientific and management disciplines. UAVs may be particularly valuable for precision agricultural applications, offering strong potential to improve the efficiency of water, nutrient, and disease management. However, some authors have suggested that the UAV industry has overhyped the potential value of this technology for agriculture, given that it is difficult for non-specialists to operate UAVs as well as to process and interpret the resulting data. Here, we analyze the barriers to applying UAVs for precision agriculture, which range from regulatory issues to technical requirements. We then evaluate how new developments in the nano- and micro-UAV (NAV and MAV, respectively) markets may help to overcome these barriers. Among the possible breakthroughs that we identify is the ability of NAV/MAV platforms to directly quantify plant traits using methods (e.g., object-oriented classification) that require less image calibration and interpretation than spectral index–based approaches. We suggest that this potential, when combined with steady improvements in sensor miniaturization, flight precision, and autonomy as well as cloud-based image processing, will make UAVs a tool with much broader adoption by agricultural managers in the near future. If this wider uptake is realized, then UAVs have real potential to improve agriculture's resource-use efficiency. © 2020 by John Wiley & Sons, Inc.","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37657907","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: 11

DNA Extraction from Plant Leaves Using a Microneedle Patch 用微针贴片提取植物叶片DNA

Current protocols in plant biology Pub Date : 2020-02-19 DOI: 10.1002/cppb.20104

Rajesh Paul, Emily Ostermann, Zhen Gu, Jean B. Ristaino, Qingshan Wei

{"title":"DNA Extraction from Plant Leaves Using a Microneedle Patch","authors":"Rajesh Paul, Emily Ostermann, Zhen Gu, Jean B. Ristaino, Qingshan Wei","doi":"10.1002/cppb.20104","DOIUrl":"10.1002/cppb.20104","url":null,"abstract":"Isolation of high-quality DNA from infected plant specimens is an essential step for the molecular detection of plant pathogens. However, DNA isolation from plant cells surrounded by rigid polysaccharide cell walls involves complicated steps and requires benchtop laboratory equipment. As a result, plant DNA extraction is currently confined to well-equipped laboratories and sample preparation has become one of the major hurdles for on-site molecular detection of plant pathogens. To overcome this hurdle, a simple DNA extraction method from plant leaf tissues has been developed. A microneedle (MN) patch made of polyvinyl alcohol (PVA) can isolate plant or pathogenic DNA from different plant species within a minute. During DNA extraction, the polymeric MN patch penetrates into plant leaf tissues and breaks rigid plant cell walls to isolate intracellular DNA. The extracted DNA is polymerase chain reaction (PCR) amplifiable without additional purification. This minimally invasive method has successfully extracted Phytophthora infestans DNA from infected tomato leaves. Moreover, the MN patch could be used to isolate DNA from other plant pathogens directly in the field. Thus, it has great potential to become a rapid, on-site sample preparation technique for plant pathogen detection. © 2020 by John Wiley & Sons, Inc.Basic Protocol: Microneedle patch-based DNA extractionSupport Protocol 1: Microneedle patch fabricationSupport Protocol 2: Real-time PCR amplification of microneedle patch extracted DNA","PeriodicalId":10932,"journal":{"name":"Current protocols in plant biology","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cppb.20104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37656887","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: 16