Legume Genomics: Methods and Protocols

Front Matter ....Pages i-xii
 Updates on Legume Genome Sequencing  (Jungmin Ha, Suk-Ha Lee)....Pages 1-18
 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
 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
 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
 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
 Method for Bisulfite Sequencing Data Analysis for Whole-Genome Level DNA Methylation Detection in Legumes  (Khushboo Gupta, Rohini Garg)....Pages 127-145
 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
 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
 Functional Genomic Selection in Crop Breeding  (Yongle Li)....Pages 189-198
 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
 Developing Transposable Element Marker System for Molecular Breeding  (R. S. Bhat, K. Shirasawa, Y. Monden, H. Yamashita, M. Tahara)....Pages 233-251
 Machine Learning-Based Annotation of Long Noncoding RNAs Using PLncPRO  (Niraj K. Khemka, Urminder Singh, Anuj K. Dwivedi, Mukesh Jain)....Pages 253-260
 Methods for Identification and Validation of G-Quadruplex Sequences in Legumes  (Surabhi Singh, Tanya Mathur, Khushboo Gupta, Rohini Garg)....Pages 261-268
 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
 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
 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
 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
 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
 CRISPR/Cas9-Based Gene Editing in Soybean  (Aili Bao, Lam-Son Phan Tran, Dong Cao)....Pages 349-364
 Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains  (Soodeh Tirnaz, Yueqi Zhang, Jacqueline Batley)....Pages 365-375
 Determination of Bioactive Compounds of Fenugreek (Trigonella foenum-graecum) Seeds Using LC-MS Techniques  (Pratibha Singh, Vikas Bajpai, Vikaskumar Gond, Ashok Kumar, Narender Tadigoppula, Brijesh Kumar)....Pages 377-393
 Quantitative Phosphoproteomic Analysis of Legume Using TiO2-Based Enrichment Coupled with Isobaric Labeling  (Pragya Barua, Nilesh Vikram Lande, Sunil Kumar, Subhra Chakraborty, Niranjan Chakraborty)....Pages 395-406
Back Matter ....Pages 407-409