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Genotyping by Sequencing for Crop Improvement
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Вернуться на страницу книги Genotyping by Sequencing for Crop Improvement
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Страница 1
Table of Contents
List of Tables
List of Illustrations
Guide
Pages
Genotyping by Sequencing for Crop Improvement
Страница 8
Страница 9
List of Contributors
Preface
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
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
2.2.2.1.1 PCR‐Free Genotyping Technology
Invader Assay
2.2.2.1.2 PCR‐based Detection System
Primer Extension Method
TaqMan SNP Genotyping
Kompetitive Allele‐Specific PCR (KASP)
rhAmp SNP Genotyping
2.2.2.1.3 Hybridization‐based Platforms or Array‐based Methods
2.2.2.1.4 Sequencing‐based Platforms
Restriction Site‐Associated DNA (RAD‐seq)
Genotyping‐by‐Sequencing (GBS)
2.2.2.2 Allelic Detection
2.2.2.2.1 Allele‐Specific Primer‐based SNP Genotyping‐Fluidigm
MALDI TOF‐based SNP Genotyping‐Sequenom
2.2.3 Custom Assay Technologies
2.2.4 Summary
References
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
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