Genotyping by Sequencing for Crop Improvement

Cover
Title Page
Copyright Page
Contents
List of Contributors
Preface
Chapter 1 Molecular Marker Techniques and Recent Advancements
1.1 Introduction
1.2 What is a Molecular Marker?
1.3 Classes of Molecular Markers
1.3.1 Hybridization-based Markers
1.3.1.1 Restriction Fragment Length Polymorphism (RFLP)
1.3.1.2 Diversity Array Technology (DArT™)
1.3.2 Polymerase Chain Reaction (PCR)-based Markers
1.3.2.1 Simple-Sequence Repeats (SSRs)
1.3.2.2 Sequence-Tagged Sites (STSs)
1.3.2.3 Randomly Amplified Polymorphic DNAs (RAPDs)
1.3.2.4 Sequence Characterized Amplified Regions (SCARs)
1.3.2.5 Amplified Fragment Length Polymorphism (AFLP)
1.3.2.6 Expressed Sequence Tags (ESTs)
1.4 Sequencing-based Markers
1.4.1 Single-Nucleotide Polymorphisms (SNPs)
1.4.2 Identification of SNP in a Pregenomic Era
1.5 Recent Advances in Molecular Marker Technologies
1.5.1 Genotyping-by-Sequencing (GBS)
1.5.2 Whole-Genome Resequencing (WGR)
1.5.3 SNP Arrays
1.5.4 Kompetitive Allele-Specific PCR (KASP™)
1.6 SNP Databases
1.7 Application of Molecular Markers
1.7.1 Application of Molecular Markers in Crop Improvement
1.7.2 Role of Molecular Markers in Germplasm Characterization
1.7.3 Deployment of Molecular Markers in Plant Variety Protection and Registration
1.8 Summary
References
Chapter 2 High-throughput Genotyping Platforms
2.1 Introduction
2.2 SNP Genotyping Platforms
2.2.1 SNP Genotyping Versus SNP Discovery
2.2.2 Types of SNP Genotyping Platforms
2.2.2.1 Allelic Discrimination
2.2.2.2 Allelic Detection
2.2.3 Custom Assay Technologies
2.2.4 Summary
References
Chapter 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
3.3.1 1K Arabidopsis Genomes Resequencing Project
3.3.2 3K Rice Genomes Resequencing Project
3.3.3 Soybean Whole-Genome Resequencing
3.3.4 Chickpea
3.3.5 Pigeon pea
3.3.6 Vitis
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
3.6.1 SNP Seek
3.6.2 Rice Functional and Genomic Breeding
3.6.3 Genome Variation Map
3.7 Applications and Successful Examples of Whole-Genome Resequencing
3.8 Challenges for Whole-Genome Resequencing Studies
3.9 Summary
References
Chapter 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
4.11.1 Nested Association Mapping (NAM)
4.11.2 Multi-advanced Generation Inter-cross Populations (MAGIC)
4.12 QTL Mapping Using Multiparental Populations
4.13 Use of High-throughput Genotyping for QTL Mapping
4.13.1 PCR-based SNP Genotyping
4.14 Next-Generation Sequencing-based Genotyping
4.14.1 Restriction-Site-Associated DNA Sequencing (RAD-seq)
4.14.2 Genotyping-by-Sequencing
4.14.3 Whole-Genome Resequencing
4.15 Challenges with QTL Mapping Using Multiparental Populations and High-throughput Genotyping
References
Chapter 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
5.8.1 Maize
5.8.2 Rice
5.8.3 Wheat
5.8.4 Barley
5.8.5 Pearl Millet
5.8.6 Sugarcane
5.9 Candidate Gene Identification at GWAS Loci
5.10 Meta-GWAS
5.11 GWAS vs. QTL Mapping
References
Chapter 6 Genotyping of Seeds While Preserving Their Viability
6.1 Introduction
6.1.1 Genotyping
6.1.2 Genotyping-by-Sequencing
6.2 Genotyping-by-Sequencing with Minimum DNA
6.3 DNA Extraction from Half Grain
6.3.1 DNA Extraction from Rice Seeds
6.3.2 DNA Extraction from Wheat and Barley Seeds
6.3.3 DNA Extraction from Maize Seeds
6.3.4 DNA Extraction from Soybean Seeds
6.3.5 DNA Extraction from Cotton Seeds
6.3.6 DNA Extraction from Papaya Seeds
6.3.7 DNA Extraction from Watermelon Seeds
6.4 GBS with Half Seed
6.5 Applications of GBS as Diagnostic Tool
6.5.1 Germplasm Conservation and Quality Control
6.5.2 Tracking Crop Varieties
6.5.3 Sex Determination
6.5.4 Transgenic Detection
6.5.5 Detection of Seed-borne Diseases
6.6 Summary
References
Chapter 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
Chapter 8 Analytical Pipelines for the GBS Analysis
8.1 Introduction
8.2 Applications of NGS
8.3 NGS Sequencing Platforms
8.3.1 Sequencing by Synthesis
8.3.1.1 Roche 454 Pyrosequencing
8.3.1.2 Illumina
8.3.1.3 Ion Torrent
8.3.2 Sequencing by Ligation
8.3.2.1 SOLiD
8.3.2.2 Polonator
8.3.3 Single-Molecule Sequencing
8.3.3.1 Helicos
8.3.3.2 Pacific Bioscience
8.3.3.3 ChIP-Sequencing
8.4 Tools for NGS Data Analysis
8.5 Generalized Procedure for NGS Data Analysis
8.5.1 Assessment of Quality
8.5.2 Aligning Sequences
8.5.3 Identification of Variants
8.6 Variant Annotation
8.6.1 Visualization of NGS Data
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
Chapter 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
9.6.1 Maize Resequencing
9.7 Genotyping-by-Sequencing-based GWAS and GS Efforts in Maize
9.8 Summary
References
Chapter 10 Recent Advances and Applicability of GBS, GWAS, and GS in Soybean
10.1 Introduction
10.1.1 Importance of Soybean for Global Food Security
10.1.2 Challenges in Soybean Production
10.1.3 Soybean Genetic Improvement
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
10.7.1 The General Procedure for Association Mapping
10.7.2 Approaches Used for Association Studies
10.8 GBS-based Genomic Selection Efforts in Soybean
References
Chapter 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
Chapter 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
12.5.1 Pearl Millet
12.5.2 Broomcorn Millet
12.5.3 Finger Millet
12.5.4 Foxtail Millet
12.5.5 Sorghum
12.6 GBS-based GWAS Efforts in Millet Crops
12.7 GBS-based Genomic Selection (GS) Efforts in Millet Crops
12.8 Summary
References
Chapter 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
Chapter 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
Chapter 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
15.7.1 Linkage Maps and Mapping Software Tools for Polyploids
15.8 Haplotype-based Genotyping
15.9 GBS Analytical Pipelines for Polyploids
15.9.1 Fast-GBS
15.9.2 PolyRAD
15.9.3 UGbS-Flex
15.9.4 HaploTag
15.10 GBS-based QTL Mapping Efforts in Polyploids
15.10.1 Wheat
15.10.2 Potato
15.10.3 Sugarcane
15.10.4 Canola
15.10.5 Peanut
15.10.6 Cotton
15.11 GWAS and GS Using High-throughput Genotyping in Polyploidy Crops
15.11.1 Wheat
15.11.2 Potato
15.11.3 Sugarcane
15.11.4 Canola
15.11.5 Peanut
15.11.6 Cotton
References
Chapter 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
16.3.1 High-density Linkage Maps for Peanut
16.3.2 High-density Linkage Maps for Sunflower
16.3.3 High-density Linkage Maps of Sesamum
16.3.4 High-density Linkage Maps of Safflower
16.3.5 High-density Linkage Maps of Linseed
16.3.6 High-density Linkage Maps of Soybean
16.3.7 High-density Linkage Maps of Rapeseed
16.4 GBS Protocols and Analytical Pipelines
16.5 GBS-based QTL Mapping Efforts in Oilseed Crops
16.5.1 GBS-based QTL in Peanut
16.5.2 GBS-based QTL in Soybean
16.5.3 GBS-based QTL in Rapeseed
16.6 GBS-based GWAS Efforts in Oilseed Crops
References
Index
EULA