1  Cover

      2  Title Page

      3  Copyright Page

      4  Dedication

      5  List of Contributors

      6  Preface

      7  1 Molecular Marker Techniques and Recent Advancements 1.1 Introduction 1.2 What is a Molecular Marker? 1.3 Classes of Molecular Markers 1.4 Sequencing‐based Markers 1.5 Recent Advances in Molecular Marker Technologies 1.6 SNP Databases 1.7 Application of Molecular Markers 1.8 Summary References

      8  2 High‐throughput Genotyping Platforms 2.1 Introduction 2.2 SNP Genotyping Platforms References

      9  3 Opportunity and Challenges for Whole‐Genome Resequencing‐based Genotyping in Plants 3.1 Introduction 3.2 Basic Steps Involved in Whole‐Genome Sequencing and Resequencing 3.3 Whole‐Genome Resequencing Mega Projects in Different Crops 3.4 Whole‐Genome Pooled Sequencing 3.5 Pinpointing Gene Through Whole‐Genome Resequencing‐based QTL Mapping 3.6 Online Resources for Whole‐Genome Resequencing Data 3.7 Applications and Successful Examples of Whole‐Genome Resequencing 3.8 Challenges for Whole‐Genome Resequencing Studies 3.9 Summary References

      10  4 QTL Mapping Using Advanced Mapping Populations and High‐throughput Genotyping 4.1 Introduction 4.2 The Basic Objectives of QTL Mapping 4.3 QTL Mapping Procedure 4.4 The General Steps for QTL Mapping 4.5 Factors Influencing QTL Analysis 4.6 QTL Mapping Approaches 4.7 Statistical Methods for QTL Mapping 4.8 Software for QTL Mapping 4.9 Bi‐parental Mapping Populations 4.10 QTL Mapping Using Bi‐parental Populations 4.11 Multiparental Mapping Populations 4.12 QTL Mapping Using Multiparental Populations 4.13 Use of High‐throughput Genotyping for QTL Mapping 4.14 Next‐Generation Sequencing‐based Genotyping 4.15 Challenges with QTL Mapping Using Multiparental Populations and High‐throughput Genotyping References

      11  5 Genome‐Wide Association Study: Approaches, Applicability, and Challenges 5.1 Introduction 5.2 Methodology to Conduct GWAS in Crops 5.3 Statistical Modeling in GWAS 5.4 Efficiency of GWAS with Different Marker Types 5.5 Computational Tools for GWAS 5.6 GWAS Challenges for Complex Traits 5.7 Factors Challenging the GWAS for Complex Traits 5.8 GWAS Applications in Major Crops 5.9 Candidate Gene Identification at GWAS Loci 5.10 Meta‐GWAS 5.11 GWAS vs. QTL Mapping References

      12  6 Genotyping of Seeds While Preserving Their Viability 6.1 Introduction 6.2 Genotyping‐by‐Sequencing with Minimum DNA 6.3 DNA Extraction from Half Grain 6.4