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
• 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.
• Sommario/riassunto: "Recent advances in sequencing technology has brought numerous opportunities for several domains of science focusing on basic as well as applied research. Plant genomics is one such domain where the shift of paradigm has been witnessed more evidently. Genotyping by sequencing (GBS) has become an indispensable tool for the plant science community. There are numerous advances making GBS more efficient for specific crops. Several technological and analytical options are available with GBS. Now, GBS is being used for day to day breeding activities, germplasm screening, diagnostic application, and basic research"--
• 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.: 9910677570503321
• Lo trovi qui: Univ. Federico II