Genotyping by Sequencing for Crop Improvement

1 Cover

2 Title Page Genotyping by Sequencing for Crop Improvement Edited by Humira Sonah National Agri‐Food Biotechnology Institute Punjab, India Vinod Goyal CCS Haryana Agriculture University Hisar, India S.M. Shivaraj Laval University Quebec City, QC, Canada Rupesh K. Deshmukh National Agri‐Food Biotechnology Institute Punjab, India

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 GBS with Half Seed 6.5 Applications of GBS as Diagnostic Tool 6.6 Summary References

13 7 Genomic Selection: Advances, Applicability, and Challenges 7.1 Introduction 7.2 Natural Selection 7.3 Breeding Selection 7.4 Marker‐assisted Selection 7.5 Genomic Selection 7.6 Genotyping for Genomic Selection 7.7 Integration of Genomic Selection in MAS Program 7.8 The Efficiency of Genomic Selection for Complex Traits 7.9 Integration of Genomic Selection in the Varietal Trial Program 7.10 Cost Comparison of GS vs MAS References

14 8 Analytical Pipelines for the GBS Analysis 8.1 Introduction 8.2 Applications of NGS 8.3 NGS Sequencing Platforms 8.4 Tools for NGS Data Analysis 8.5 Generalized Procedure for NGS Data Analysis 8.6 Variant Annotation 8.7 Role of NGS Informatics in Identifying Variants 8.8 Genotyping by Sequencing 8.9 Analytical Pipelines for GBS 8.10 Comparison of GBS Pipelines References

15 9 Recent Advances and Applicability of GBS, GWAS, and GS in Maize 9.1 Introduction 9.2 Maize Genetics 9.3 Importance of Genomics and Genotyping‐based Applications in Maize Breeding Programs 9.4 GBS‐based QTL Mapping in Maize 9.5 GBS Protocols and Analytical Pipelines for Maize 9.6 Maize Genome Sequencing and Resequencing 9.7 Genotyping‐by‐Sequencing‐based GWAS and GS Efforts in Maize 9.8 Summary References

16 10 Recent Advances and Applicability of GBS, GWAS, and GS in Soybean 10.1 Introduction 10.2 GBS Efforts in Soybean 10.3 High‐Density Linkage Maps in Soybean 10.4 GBS Protocols and Analytical Pipelines for Soybean 10.5 GBS‐based QTL Mapping Efforts in Soybean 10.6 Soybean Genome Sequencing and Resequencing 10.7 GBS‐based GWAS Efforts in Soybean 10.8 GBS‐based Genomic Selection Efforts in Soybean References

17 11 Advances and Applicability of Genotyping Technologies in Cotton Improvement 11.1 Introduction 11.2 Challenges due to Polyploidy in Cotton 11.3 Applications of Genomics and Genotyping for Cotton Breeding Programs 11.4 Genotyping Efforts in Cotton 11.5 High‐Density Linkage Maps in Cotton 11.6 Whole‐Genome Sequencing of Cotton Germplasm 11.7 Application of GBS Technology in Cotton Research 11.8 GBS‐based Bi‐Parental QTL Mapping and Association Mapping in Cotton 11.9 Summary and Outlook References

18 12 Recent Advances and Applicability of GBS, GWAS, and GS in Millet Crops * 12.1 Introduction 12.2 GBS Efforts in Millet Crops 12.3 High‐density Linkage Maps in Millet Crops 12.4 GBS‐based QTL Mapping Efforts in Millet Crops 12.5 Genome Sequencing and Resequencing of Millet Crops 12.6 GBS‐based GWAS Efforts in Millet Crops 12.7 GBS‐based Genomic Selection (GS) Efforts in Millet Crops 12.8 Summary References

19 13 Recent Advances and Applicability of GBS, GWAS, and GS in Pigeon Pea 13.1 Introduction 13.2 Pigeon Pea Sequencing and Resequencing 13.3 Development of Pigeon Pea High‐density Genotyping Platforms 13.4 Development of High‐density Linkage Maps in Pigeon Pea 13.5 QTL Analysis Using High‐density Genotyping Platforms and GBS 13.6 GWAS Efforts in Pigeon Pea 13.7 Genomic Selection (GS) Efforts in Pigeon Pea 13.8 Summary References

20 14 Opportunity and Challenges for High‐throughput Genotyping in Sugarcane 14.1 Introduction 14.2 Sugarcane Genome and Genetics 14.3 Genetic Studies and Marker Systems 14.4 Genotyping‐by‐Sequencing (GBS) 14.5 SNP Calling Using GBS Pipelines 14.6 Sugarcane Genome Sequencing 14.7 Linkage and QTL Mapping in Sugarcane 14.8 GWAS in Sugarcane 14.9 Genomic Selection in Sugarcane 14.10 Summary References

21 15 Recent Advances and Applicability of GBS, GWAS, and GS in Polyploid Crops 15.1 Introduction 15.2 Challenges for Genotyping in Polyploidy Crops 15.3 Genotyping Platforms for Barley 15.4 Long‐Read Sequencing‐based Genotyping in Polyploid Canola 15.5 Peanut Genotyping with Targeted Amplicon Sequencing 15.6 SNP Genotyping Methods and Platforms Available for Sugarcane 15.7 Recent Advances and Applicability of GBS, GWAS, and GS in Polyploidy Crop Species 15.8 Haplotype‐based Genotyping 15.9 GBS Analytical Pipelines for Polyploids 15.10 GBS‐based QTL Mapping Efforts in Polyploids 15.11 GWAS and GS Using High‐throughput Genotyping in Polyploidy Crops References

22 16 Recent Advances and Applicability of GBS, GWAS, and GS in Oilseed Crops 16.1 Introduction 16.2 GBS Efforts in Oilseed Crops 16.3 High‐density Linkage Maps for Oilseed Crops 16.4 GBS Protocols and Analytical Pipelines 16.5 GBS‐based QTL Mapping Efforts in Oilseed Crops 16.6 GBS‐based GWAS Efforts in Oilseed Crops References

23 Index

24 End User License Agreement

1 Chapter 1 Table 1.1 Details of the other important molecular markers. Table 1.2 Comparison between different marker techniques commonly used in p... Table 1.3 List of important online SNP databases.