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Plant Genotyping

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Yuri Shavrukov

    1. College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia

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  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2638)

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Table of contents (32 protocols)

  1. Front Matter

    Pages i-xvi
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  2. Genotyping by Sequencing (GBS) for Genome-Wide SNP Identification in Plants

    • Wirulda Pootakham
    Pages 1-8

  3. Genotyping by Multiplexed Sequencing (GMS) Using SNP Markers

    • Travis M. Ruff, Karol Marlowe, Marcus A. Hooker, Yan Liu, Deven R. See
    Pages 9-21

  4. Computational Protocol for DNA Methylation Profiling in Plants Using Restriction Enzyme-Based Genome Reduction

    • Wendell Jacinto Pereira, Marília de Castro Rodrigues Pappas, Georgios Joannis Pappas Jr.
    Pages 23-36

  5. Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq) Technology

    • Natalia Cristina Aguirre, Carla Valeria Filippi, Pablo Alfredo Vera, Andrea Fabiana Puebla, Giusi Zaina, Verónica Viviana Lia et al.
    Pages 37-57

  6. Whole Genome Wide SSR Markers Identification Based on ddRADseq Data

    • Gitanjali Tandon, Sarika Jaiswal, Mir Asif Iquebal, Anil Rai, Dinesh Kumar
    Pages 59-66

  7. High-Throughput Association Mapping in Brassica napus L.: Methods and Applications

    • Rafaqat Ali Gill, Md Mostofa Uddin Helal, Minqiang Tang, Ming Hu, Chaobo Tong, Shengyi Liu
    Pages 67-91

  8. Polyploid SNP Genotyping Using the MassARRAY System

    • Aline da Costa Lima Moraes, Danilo Augusto Sforça, Melina Cristina Mancini, Bianca Baccili Zanotto Vigna, Anete Pereira de Souza
    Pages 93-113

  9. qPCR Genotyping of Polyploid Species

    • Haiyan Wang, Jiangbo Dang, Qigao Guo, Guolu Liang
    Pages 115-122

  10. Genome-Wide Association Studies (GWAS)

    • Jianbo He, Junyi Gai
    Pages 123-146

  11. Transcriptomic Approach for Global Distribution of SNP/Indel and Plant Genotyping

    • Claudia Muñoz-Espinoza, Marco Meneses, Patricio Hinrichsen
    Pages 147-164

  12. Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

    • Yang Zhou, Huitang Pan
    Pages 165-171

  13. Modifications of Kompetitive Allele-Specific PCR (KASP) Genotyping for Detection of Rare Alleles

    • Anthony Brusa, Eric Patterson, Margaret Fleming
    Pages 173-189

  14. Amplifluor-Based SNP Genotyping

    • Manmode Darpan Mohanrao, Senapathy Senthilvel, Yarabapani Rushwanth Reddy, Chippa Anil Kumar, Palchamy Kadirvel
    Pages 191-200

  15. SNP Genotyping with Amplifluor-Like Method

    • Gulmira Khassanova, Sholpan Khalbayeva, Dauren Serikbay, Shynar Mazkirat, Kulpash Bulatova, Maral Utebayev et al.
    Pages 201-219

  16. Semi-Thermal Asymmetric Reverse PCR (STARP) Genotyping

    • Awais Rasheed
    Pages 221-230

  17. Modified Allele-Specific qPCR (ASQ) Genotyping

    • Aigul Amangeldiyeva, Akmaral Baidyussen, Marzhan Kuzbakova, Raushan Yerzhebayeva, Satyvaldy Jatayev, Yuri Shavrukov
    Pages 231-247

  18. Allele-Specific Mutation Genotyping with Mismatches in Primer Design

    • Yutaro Saito, Fumito Tada, Tadashi Takashina, Hidetoshi Ikegami
    Pages 249-262

  19. PCR Allele Competitive Extension (PACE)

    • Daniel von Maydell
    Pages 263-271

  20. Molecular Beacon Probe (MBP)-Based Real-Time PCR

    • Gopal Kumar Prajapati, Ashutosh Kumar, Aakanksha Wany, Dev Mani Pandey
    Pages 273-287
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Keywords

About this book

This thorough volume presents a wide range of existing methods, from the very popular to the more exotic, in the area of plant genotyping. Many methods of plant genotyping were initially developed for medical research, but all genotyping methods, if they are to be successful, should be suitable for application across the full range of studies within plant biology, as seen in this collection. Plant genotyping methods herein are based on a variety of assessments, including DNA microarray, with its hundreds of thousands of simultaneous reactions, or separate individual studies of DNA sequencing and fragment analysis, PCR and qPCR, allele-specific molecular probes and primers, digestion with restriction endonucleases, microscopy and many others. 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, andtips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Plant Genotyping: Methods and Protocols offers researchers the opportunity to update their knowledge and choose the most suitable method of plant genotyping for their chosen application.

Editors and Affiliations

  • College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia

    Yuri Shavrukov

Bibliographic Information

  • Book Title: Plant Genotyping

  • Book Subtitle: Methods and Protocols

  • Editors: Yuri Shavrukov

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3024-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-3023-5Published: 14 February 2023

  • Softcover ISBN: 978-1-0716-3026-6Published: 14 February 2024

  • eBook ISBN: 978-1-0716-3024-2Published: 13 February 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 469

  • Number of Illustrations: 92 b/w illustrations

  • Topics: Plant Sciences, Plant Genetics and Genomics, Ecology

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