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Legume Genomics

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. Mukesh Jain

    1. School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India

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    You can also search for this editor in PubMed   Google Scholar

  2. Rohini Garg

    1. Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, India

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2107)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xii
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  2. Updates on Legume Genome Sequencing

    • Jungmin Ha, Suk-Ha Lee
    Pages 1-18

  3. Updates on Genomic Resources in Chickpea for Crop Improvement

    • Rajesh Ghangal, Vikash K. Singh, Niraj K. Khemka, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
    Pages 19-33

  4. Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach

    • Haifei Hu, Yuxuan Yuan, Philipp E. Bayer, Cassandria T. Fernandez, Armin Scheben, Agnieszka A. Golicz et al.
    Pages 35-47

  5. Methods and Tools for Plant Organelle Genome Sequencing, Assembly, and Downstream Analysis

    • Sanand Sandhya, Harsha Srivastava, Tanvi Kaila, Anshika Tyagi, Kishor Gaikwad
    Pages 49-98

  6. Methods of Gene Expression Profiling to Understand Abiotic Stress Perception and Response in Legume Crops

    • Meenu Bala, Ragini Sinha, M. A. Mallick, Tilak Raj Sharma, Anil Kumar Singh
    Pages 99-126

  7. Method for Bisulfite Sequencing Data Analysis for Whole-Genome Level DNA Methylation Detection in Legumes

    • Khushboo Gupta, Rohini Garg
    Pages 127-145

  8. Method for Genome-Wide Association Study: A Soybean Example

    • Robyn Anderson, Cassandria Tay Fernandez, Yuxuan Yuan, Agnieszka A. Golicz, David Edwards, Philipp E. Bayer
    Pages 147-158

  9. Genotyping for Species Identification and Diversity Assessment Using Double-Digest Restriction Site-Associated DNA Sequencing (ddRAD-Seq)

    • Anita A. Severn-Ellis, Armin Scheben, Ting Xiang Neik, Nur Shuhadah Mohd Saad, Aneeta Pradhan, Jacqueline Batley
    Pages 159-187

  10. Functional Genomic Selection in Crop Breeding

    • Yongle Li
    Pages 189-198

  11. Methods for Target Enrichment Sequencing via Probe Capture in Legumes

    • Ze Peng, Dev Paudel, Liping Wang, Ziliang Luo, Qian You, Jianping Wang
    Pages 199-231

  12. Developing Transposable Element Marker System for Molecular Breeding

    • R. S. Bhat, K. Shirasawa, Y. Monden, H. Yamashita, M. Tahara
    Pages 233-251

  13. Machine Learning-Based Annotation of Long Noncoding RNAs Using PLncPRO

    • Niraj K. Khemka, Urminder Singh, Anuj K. Dwivedi, Mukesh Jain
    Pages 253-260

  14. Methods for Identification and Validation of G-Quadruplex Sequences in Legumes

    • Surabhi Singh, Tanya Mathur, Khushboo Gupta, Rohini Garg
    Pages 261-268

  15. Method for Characterization of Root Traits in Chickpea Germplasm for Legume Genomics and Breeding

    • Yinglong Chen, Tao Zhou, Kadambot H. M. Siddique
    Pages 269-275

  16. Methods for Screening Legume Crops for Abiotic Stress Tolerance through Physiological and Biochemical Approaches

    • Ragini Sinha, Meenu Bala, Madan Kumar, Tilak Raj Sharma, Anil Kumar Singh
    Pages 277-303

  17. An Efficient Method of Mitochondrial DNA Isolation from Vigna radiata for Genomic Studies

    • Pooja Singh, Ranjan Kumar Sahoo, Mallesham Bulle, Kapuganti Jagadis Gupta
    Pages 305-315

  18. Embryonic Explant and Plumular Meristem Transformation Methods for Development of Transgenic Pigeon Pea

    • Shreeparna Ganguly, Arnab Purohit, Rituparna Kundu Chaudhuri, Sampa Das, Dipankar Chakraborti
    Pages 317-333

  19. Optimization of Hairy Root Transformation for the Functional Genomics in Chickpea: A Platform for Nodule Developmental Studies

    • Drishti Mandal, Deevita Srivastava, Senjuti Sinharoy
    Pages 335-348

  20. CRISPR/Cas9-Based Gene Editing in Soybean

    • Aili Bao, Lam-Son Phan Tran, Dong Cao
    Pages 349-364
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Keywords

About this book

This volume looks at the latest techniques used by researchers to help them understand the biology of various cellular processes and agronomic traits, and come up with better strategies to improve legume crops. The chapters in this book cover topics such as legume genomic resources; legume pangenome and organelle genome construction; transcriptome analysis; DNA methylation analysis; double-digest restriction site-associated DNA sequencing; target enrichment sequencing via probe capture; genomic selection and transformation methods; prediction of long non-coding RNAs and secondary structures; genome-wide mining of disease resistance gene analogs; genome editing, and bioactive compound and phosphoproteome analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.


Cutting-edge and informative, Legume Genomics: Methods and Protocols is a useful reference for genomicists, molecular breeders, plant molecular biologists, biotechnologists, computational biologists, and developmental biologists. This book is also an excellent resource for any novice and expert researcher involved in various molecular aspects of legume biology or general plant studies.


Editors and Affiliations

  • School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India

    Mukesh Jain

  • Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, India

    Rohini Garg

Bibliographic Information

  • Book Title: Legume Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: Mukesh Jain, Rohini Garg

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0235-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0234-8Published: 01 January 2020

  • Softcover ISBN: 978-1-0716-0237-9Published: 01 January 2021

  • eBook ISBN: 978-1-0716-0235-5Published: 31 December 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 409

  • Number of Illustrations: 32 b/w illustrations, 49 illustrations in colour

  • Topics: Plant Sciences, Plant Genetics and Genomics

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