Genotyping by Sequencing for Crop Improvement

Description

OGENOTYPING BY SEQUENCING FOR CROP IMPROVEMENT A thoroughly up-to-date exploration of genotyping-by-sequencing technologies and related methods in plant science In Genotyping by Sequencing for Crop Improvement, a team of distinguished researchers delivers an in-depth and current exploration of the latest advances in genotyping-by-sequencing (GBS) methods, the statistical approaches used to analyze GBS data, and its applications, including quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS) in crop improvement. This edited volume includes insightful contributions on a variety of relevant topics, like advanced molecular markers, high-throughput genotyping platforms, whole genome resequencing, QTL mapping with advanced mapping populations, analytical pipelines for GBS analysis, and more. The distinguished contributors explore traditional and advanced markers used in plant genotyping in extensive detail, and advanced genotyping platforms that cater to unique research purposes are discussed, as is the whole-genome resequencing (WGR) methodology. The included chapters also examine the applications of these technologies in several different crop categories, including cereals, pulses, oilseeds, and commercial crops. Genotyping by Sequencing for Crop Improvement also offers: A thorough introduction to molecular marker techniques and recent advancements in the technologyComprehensive explorations of the genotyping of seeds while preserving their viability, as well as advances in genomic selectionPractical discussions of opportunities and challenges relating to high throughput genotyping in polyploid cropsIn-depth examinations of recent advances and applications of GBS, GWAS, and GS in cereals, pulses, oilseeds, millets, and commercial crops Perfect for practicing plant scientists with an interest in genotyping-by-sequencing technology, Genotyping by Sequencing for Crop Improvement will also earn a place in the libraries of researchers and students seeking a one-stop reference on the foundational aspects of – and recent advances in – genotyping-by-sequencing, genome-wide association studies, and genomic selection. 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