Legume Genomics: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

1. Updates on Legume Genome Sequencing
Jungmin Ha and Suk-Ha Lee

2. Updates on Genomic Resources in Chickpea for Crop Improvement
Rajesh Ghangal, Vikash K. Singh, Niraj Khemka, Mohan Singh Rajkumar, Rohini Garg, and Mukesh Jain

3. Legume Pangenome Construction using an Iterative Mapping and Assembly Approach
Haifei Hu, Yuxuan Yuan, Philipp E. Bayer, Cassandria T Fernandez, Armin Scheben, Agnieszka Golicz, and David Edwards

4. Methods and Tools for Plant Organelle Genome Sequencing, Assembly and Downstream Analysis
Sandhya, Harsha Srivastava, Tanvi Kaila, Anshika Tyagi, and Kishor Gaikwad

5. 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, and Anil Kumar Singh

6. Method for Bisulphite Sequencing Data Analysis for Whole Genome Level DNA Methylation Detection in Legumes
Khushboo Gupta and Rohini Garg

7. Method for Genome-Wide Association Study: A Soybean Example
Robyn Anderson, Cassandria Tay Fernandez, Yuxuan Yuan, Agnieszka A. Golicz, David Edwards, and Philipp E. Bayer

8. 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, and Jacqueline Batley

9. Functional Genomic Selection in Crop Breeding
Yongle Li

10. Methods for Target Enrichment Sequencing via Probe Capture in Legumes
Ze Peng, Dev Paudel, Liping Wang, Ziliang Luo, Qian You, and Jianping Wang

11. Developing Transposable Element Marker System for Molecular Breeding
R. S. Bhat, K. Shirasawa, Y. Monden, H. Yamashita, and M. Tahara

12. Machine-Learning Based Annotation of Long Non-Coding RNAs using PLncPRO
Niraj K. Khemka, Urminder Singh, Anuj K. Dwivedi, and Mukesh Jain

13. Methods for Identification and Validation of G-Quadruplex Sequences in Legumes
Surabhi Singh, Tanya Mathur, Khushboo Gupta, and Rohini Garg

14. Method for Characterization of Root Traits in Chickpea Germplasm for Legume Genomics and Breeding
Yinglong Chen, Tao Zhou, and Kadambot H.M. Siddique

15. Method of Screening Legume Crops for Abiotic Stress Tolerance through Physiological and Biochemical Approaches
Ragini Sinha, Meenu Bala, Madan Kumar, Tilak Raj Sharma, and Anil Kumar Singh

16. An Efficient Method of Mitochondrial DNA Isolation from Vigna radiata for Genomic Studies
Pooja Singh, Ranjan Kumar Sahoo, Mallesham Bulle, and Kapuganti Jagadis Gupta

17. Embryonic Explant and Plumular Meristem Transformation Methods for Development of Transgenic Pigeonpea
Shreeparna Ganguly, Arnab Purohit, Rituparna Kundu Chaudhuri, Sampa Das, and Dipankar Chakraborti

18. Optimization of Hairy Root Transformation for the Functional Genomics in Chickpea: A Platform for Nodule Developmental Studies
Drishti Mandal, Deevita Srivastava, and Senjuti Sinharoy

19. CRISPR/Cas9-Based Gene Editing in Soybean
Aili Bao, Lam-Son Phan Tran, and Dong Cao

20. Genome-Wide Mining of Disease Resistance Gene Analogs using Conserved Domains
Soodeh Tirnaz, Yueqi Zhang, and Jacqueline Batley

21. Determination of Bioactive Compounds of Fenugreek (Trigonella foenum-graecum) Seeds using LC-MS Techniques
Pratibha Singh, Vikas Bajpai, Vikaskumar Gond, Ashok Kumar, Narender Tadigoppula, and Brijesh Kumar

22. Quantitative Phosphoproteomic Analysis of Legume using TiO2-Based Enrichment Coupled with Isobaric Labeling
Pragya Barua, Nilesh Vikram Lande, Sunil Kumar, Subhra Chakraborty, and Niranjan Chakraborty