Includes cutting-edge techniques
Provides step-by-step detail essential for reproducible results
Contains key implementation advice from the experts
This detailed book gathers hands-on techniques to characterize, identify, localize, profile, and determine genome functions in plants. Volume 1 opens with a section exploring protocols to advance our understanding of plant genetics and ecology via phenomics, and it continues with chapters on plant genetics, tranillegalscriptomics, and proteomics to unravel plant protein structures and functions, bridging proteomics and phosphoproteomics. Written for the highly successful
Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and comprehensive, Plant Functional Genomics: Methods and Protocols serves as an ideal guide to the immense promise of functional genomics, spanning from fundamental evolutionary studies to practical advancements in crop improvement.
Part I: Phenomics
1. An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management
Wanneng Yang, Hui Feng, Xiao Hu, Jingyan Song, Jing Guo, and Bingjie Lu
2. A High-Throughput Approach for Photosynthesis Studies in a Brassicaceae Panel
Sofia A. Bengoa Luoni, Francesco Garassino, and Mark G.M. Aarts
3. Methods for Functional Physiological Phenotyping and High-Order Data Quantification
Ting Sun, Rujia Jiang, Yunxiu Liu, and Pei Xu
4. Physiotyping of Plants and Modeling the Soil Plant Atmospheric Continuum (SPAC)
Gert Bachmann and Franz Hadacek
5. Root Hair Imaging Using Confocal Microscopy
Krishna Vasant Mutanwad, Monika Debreczeny, and Doris Lucyshyn
6. Cytogenetic Bioindication in Root Meristems for Vitality Assessment of Trees Anna Gasperl and Maria Müller
Part II: Genomics
7. Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data
Jose P. Jiménez-Madrigal, Bradley J. Till, and Andrés Gatica-Arias
8. Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data
Bradley J. Till, Jose P. Jiménez-Madrigal, and Andrés Gatica-Arias
9. Identification of Induced Copy Number Variation from Low Coverage Sequence Data
Bradley J. Till
10. Genetic Map Construction Using F2 and RIL/DH Mapping Population
Beata Mysków, Pawel Milczarski, and Stefan Stojalowski
11. QTL Mapping Using RIL Population
Pawel Milczarski, Stefan Stojalowski, and Beata Mysków
12. Sample and Library Preparation for PacBio Long Read Sequencing in Grapevine
Hymavathi Salava, Tamás Deák, Carmen Czepe, and Fatemeh Maghuly
Part III: Tranillegalscriptomics
13. RNA Isolation Method in Marginal Crops with High Agronomic Potential
Kena Casarrubias Castillo, John Délano Frier, and Paola Andrea Palmeros Suárez
14. A General Protocol for Gene Expression Analysis in Chemically Mutant Coffee Plants in Response to Rust (Hemileia vastatrix Berk & Broome) Infection
Andrés Gatica-Arias, Carolina Muñoz-Flores, and Alejandro Bolívar-González
15. Tranillegalscriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example
Thiely Patricia Fabian Dos Santos, Elodia Sánchez-Barrantes, Luiz Filipe Pereira, and Andrés Gatica-Arias
16. Quantitative Estimation of Promoter Activity in Cannabis sativa Using Agroinfiltration-Based Transient Gene Expression
Jan Fousek, Jakub Dušek, Hana Hoffmeisterová, Noemi Cerovská, Jiban Kumar Kundu, and Tomáš Moravec
Part IV: Proteomics
17. Indophenol Blue Colorimetric Method to Determine Grain Protein Content of Cereal Plants
Cheng Huang, Mutian Gao, Hongbing Luo, and Ying Xu
18. One-Dimensional Acrylamide Gel Electrophoresis for Analysis of Plant Samples
Gorji Marzban and Donatella Tesei
19. Two-Dimensional Gel Electrophoresis for Separation of Plant Samples
Gorji Marzban and Donatella Tesei
20. Sample Preparation and Phosphopeptide Enrichment for Plant Phosphoproteomics via Label-Free Mass Spectrometry
Gorji Marzban and Eldi Sulaj
21. Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf
Aswathy Jayasree, Hymavathi Salava, Tomasz Nodzynski, and Sravankumar Thula
22. Determining Macromolecular Structures Using Cryo-Electron Microscopy
Pradeep Hiriyur Nagaraj and Sudhir Kumar Pal
23. Determining Protein Structures Using X-Ray Crystallography
Subhash Narasimhan
This detailed book gathers hands-on techniques to characterize, identify, localize, profile, and determine genome functions in plants. Volume 1 opens with a section exploring protocols to advance our understanding of plant genetics and ecology via phenomics, and it continues with chapters on plant genetics, tranillegalscriptomics, and proteomics to unravel plant protein structures and functions, bridging proteomics and phosphoproteomics. Written for the highly successful
Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and comprehensive,
Plant Functional Genomics: Methods and Protocols serves as an ideal guide to the immense promise of functional genomics, spanning from fundamental evolutionary studies to practical advancements in crop improvement.
An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management.- A High-Throughput Approach for Photosynthesis Studies in a Brassicaceae Panel.- Methods for Functional Physiological Phenotyping and High-Order Data Quantification.- Physiotyping of Plants and Modeling the Soil Plant Atmospheric Continuum (SPAC).- Root Hair Imaging Using Confocal Microscopy.- Cytogenetic Bioindication in Root Meristems for Vitality Assessment of Trees.- Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.- Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data.- Identification of Induced Copy Number Variation from Low Coverage Sequence Data.- Genetic Map Construction Using F2 and RIL/DH Mapping Population.- QTL Mapping Using RIL Population.- Sample and Library Preparation for PacBio Long Read Sequencing in Grapevine.- RNA Isolation Method in Marginal Crops with High Agronomic Potential.- A General Protocol for Gene Expression Analysis in Chemically Mutant Coffee Plants in Response to Rust (Hemileia vastatrix Berk & Broome) Infection.- Tranillegalscriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example.- Quantitative Estimation of Promoter Activity in Cannabis sativa Using Agroinfiltration-Based Transient Gene Expression.- Indophenol Blue Colorimetric Method to Determine Grain Protein Content of Cereal Plants.- One-Dimensional Acrylamide Gel Electrophoresis for Analysis of Plant Samples.- Two-Dimensional Gel Electrophoresis for Separation of Plant Samples.- Sample Preparation and Phosphopeptide Enrichment for Plant Phosphoproteomics via Label-Free Mass Spectrometry.- Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf.- Determining Macromolecular Structures Using Cryo-Electron Microscopy.- Determining Protein Structures Using X-Ray Crystallography.
Inhaltsverzeichnis
An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management.- A High-Throughput Approach for Photosynthesis Studies in a Brassicaceae Panel.- Methods for Functional Physiological Phenotyping and High-Order Data Quantification.- Physiotyping of Plants and Modeling the Soil Plant Atmospheric Continuum (SPAC).- Root Hair Imaging Using Confocal Microscopy.- Cytogenetic Bioindication in Root Meristems for Vitality Assessment of Trees.- Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.- Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data.- Identification of Induced Copy Number Variation from Low Coverage Sequence Data.- Genetic Map Construction Using F2 and RIL/DH Mapping Population.- QTL Mapping Using RIL Population.- Sample and Library Preparation for PacBio Long Read Sequencing in Grapevine.- RNA Isolation Method in Marginal Crops with High Agronomic Potential.- A General Protocol for Gene Expression Analysis in Chemically Mutant Coffee Plants in Response to Rust (Hemileia vastatrix Berk & Broome) Infection.- Tranillegalscriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example.- Quantitative Estimation of Promoter Activity in Cannabis sativa Using Agroinfiltration-Based Transient Gene Expression.- Indophenol Blue Colorimetric Method to Determine Grain Protein Content of Cereal Plants.- One-Dimensional Acrylamide Gel Electrophoresis for Analysis of Plant Samples.- Two-Dimensional Gel Electrophoresis for Separation of Plant Samples.- Sample Preparation and Phosphopeptide Enrichment for Plant Phosphoproteomics via Label-Free Mass Spectrometry.- Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf.- Determining Macromolecular Structures Using Cryo-Electron Microscopy.- Determining Protein Structures Using X-Ray Crystallography.
Klappentext
This detailed book gathers hands-on techniques to characterize, identify, localize, profile, and determine genome functions in plants. Volume 1 opens with a section exploring protocols to advance our understanding of plant genetics and ecology via phenomics, and it continues with chapters on plant genetics, tranillegalscriptomics, and proteomics to unravel plant protein structures and functions, bridging proteomics and phosphoproteomics. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and comprehensive, Plant Functional Genomics: Methods and Protocols serves as an ideal guide to the immense promise of functional genomics, spanning from fundamental evolutionary studies to practical advancements in crop improvement.
