Genotyping by sequencing for crop improvement / / edited by Humira Sonah [and three others]

• Pubblicazione: Hoboken, New Jersey : , : John Wiley & Sons, , [2021]; ©2021
• Descrizione fisica: 1 online resource (402 pages)
• Disciplina: 572.862
• Soggetto topico: Gene mapping; Genetics - Technique; Genomics
• Soggetto genere / forma: Electronic books.
• Persona (resp. second.): SonahHumira
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: 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.
• Titolo autorizzato: Genotyping by Sequencing for Crop Improvement
• ISBN: 1-119-74568-3; 1-119-74566-7; 1-119-74567-5
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Lingua di pubblicazione: Inglese
• Record Nr.: 9910566698603321
• Lo trovi qui: Univ. Federico II