Potato Improvement in the Post-Genomics Era

Description

The book delves into post-genomics advances in potato improvement since the potato genome sequencing in 2011. It includes recent developments in the field of potato genetic resources, genes and SNP markers discovery, and the progress in next-generation breeding applying various omics technologies and modern sequencing tools. It covers cutting-edge technologies in potato - a global perspective, genome sequencing and resequencing of various cultivated and wild species, potato germplasm management and characterization, prebreeding genomics, genome mapping and gene cloning, markers discovery, marker-assisted selection, transgenics, microRNAs, transcriptomics, proteomics, metabolomics, phenomics, next-generation potato breeding technologies including genome editing and genomic selection and bioinformatics applications in the post-genomics era in potato. As genome editing and genomic selection have become emerging tools in crop improvement including potato, several research works have been demonstrated and applied world over. This book concentrates on genomics-aided characterization of germplasm and markers discovery to accelerate potato breeding. Further, various omics technologies strengthen our understanding on discovery of new genes/proteins/metabolites and key traits based on high-throughput phenotyping involved in various biotic and abiotic stresses in potato crop. The book is a useful source of information related to genomics-led research and development of this crop. It will serve as a valuable resource for potato researchers working in the area of molecular biology and would be beneficial for college students, PhD scholars, scientists, academicians, farmers and policy makers. Cover Series Page Title Page Copyright Page Preface to the Series Preface Dedication Foreword Table of Contents 1. Potato: A Global Scenario and Omics Research 1. Introduction 2. Global Scenario of Potato Production 3. Potato Supply, Consumption and Utilization 3.1 Fresh Potato 3.2 Processed, Seed and Loss of Potatoes 3.3 Potato Export 4. Biotic Stress in Potato 4.1 Late Blight 4.2 Viruses 4.3 Soil and Tuber-borne Diseases 4.4 Insect-pests 5. Abiotic Stresses 5.1 Heat Stress 5.2 Drought Stress 5.3 Nutrient Stress and Salinity 5.4 Frost Stress 6. Challenges in Potato 6.1 Climate Change and Rising Temperature 6.2 Broadening of Genetic Base and Productivity Enhancement 6.3 Sustainable Production System 6.4 Post-harvest Management 6.5 Integrated Disease and Insect-pest Management 7. Conclusion 2. Potato Genome Sequencing and Resequencing of Wild/Cultivated Species 1. The Potato 2. Genome Sequencing Technologies 2.1 Structural Genomics 2.2 First-generation Sequencing Technology 2.3 Next Generation Sequencing Technology 2.3.1 Roche 454 Pyrosequencing 2.3.2 Illumina 2.3.3 SOLiD (Sequencing by Oligo Ligation and Detection) 2.3.4 Ion Torrent 2.3.5 Complete Genomics Technology 2.4 Third Generation Sequencing Technology 2.4.1 PacBio 2.4.2 Oxford Nanopore 2.4.3 Mapping of Long Reads to Optical Maps 2.5 Fourth Generation Sequencing 3. The Potato Genome Sequence 4. Genome Resequencing of Wild/Cultivated Potatoes (Solanum spp.) 4.1 Impact of Post-genome Sequencing 4.2 Genome Sequence of Wild Species S. commersonii 4.3 Genome Sequence of Wild Species S. chacoense (M6) 4.4 Genome-based Structural Variation Analysis in Potato Species 4.5 Genome-aided Domestication Study in Potato Species 4.6 Genome Sequence Using Long Read Third Generation Sequencing Technology 4.7 Genome Sequence of Potato Somatic Hybrid, Parents and Progeny 5. Conclusion 3. Genomics in Potato Germplasm Management and Utilization 1. Introduction 2. Taxonomy, Origin and Domestication of Potato 2.1 Taxonomic Classification 2.2 Origin and Domestication 2.3 Cultivated and Wild Potato Species 2.3.1 Cultivated Potato Species 2.3.2 Wild Potato Species 2.4 Potato Genepool and Crossability 3. Germplasm Conservation 3.1 Potato Genebanks 3.2 In Vitro Conservation 3.3 Cryo-conservation 3.4 In Situ Conservation 4. Germplasm Characterization 4.1 Genetic Diversity by Molecular Markers 4.2 Evaluation for Agronomic Traits and Biotic and Abiotic Stresses 5. Application of Genomics in Germplasm Characterization 5.1 Germplasm Collection and Genotyping 5.2 Core Collection 6. Conclusion 4. Molecular Markers, Mapping and Genome-wide Characterization 1. Introduction 2. Molecular Markers 3. Genomic Markers for High-throughput Genotyping 3.1 Single Nucleotide Polymorphism (SNP) 3.2 Genotyping by Sequencing (GBS) 3.3 Diversity Arrays Technology (DArT) 4. Genome Mapping and Gene/QTL Discovery 4.1 Genetic and Physical Maps 4.2 Gene/QTL Mapping 4.3 High-density Genome Maps Using SNP Markers 4.3.1 Phenotypes and Tuber Traits 4.3.2 SNP in Tetraploid Allelic Doses and Double Reduction Analysis 4.3.3 Processing Quality and Other Traits 4.3.4 Disease Resistance 5. Genome-Wide Association Studies (GWAS) 5.1 Phenotypes and Yield-contributing Traits 5.1.1 Agronomic and Tuber Traits 5.1.2 Tuber Yield and Starch Content 5.1.3 Plant Maturity and Tuber Flesh Color 5.2 Germplasm Diversity and Population Structure 5.2.1 Columbian Germplasm 5.2.2 The USA Germplasm 5.2.3 The International Potato Centre (CIP) Germplasm 5.2.4 European Germplasm 5.3 Population Structure Based on Genome/Transcriptome Sequence Data 5.4 Disease Resistance 5.4.1 Potato Cyst Nematode 5.4.2 Potato Wart 5.4.3 Late Blight 5.4.4 Common Scab 5.5 Processing Traits 5.5.1 Tuber Starch Content 5.5.2 Starch Phosphate Content 5.5.3 Fry Color 5.5.4 Protein and Folate Content 5.5.5 Flower Color 6. Conclusion 5. Conventional to Genomics-assisted Breeding 1. Conventional Breeding 2. Considerations in Breeding 2.1 Parent Selection 2.2 Progeny Test 2.3 Flowering and Hybridization 2.4 Berry Harvesting and TPS Extraction 2.5 Seedling Raising and Clonal Selection 3. Breeding Strategies 4. Speed Breeding 5. Marker-Assisted Selection 6. MAS for Biotic Stress Resistance 6.1 Late Blight Resistance 6.2 Virus Resistance 6.3 Potato Cyst Nematodes Resistance 7. MAS for Abiotic Stress Tolerance and Quality Traits 7.1 Drought Stress 7.2 Cold/Low Temperature Stress 7.3 Tuber Quality Traits 8. Genomic Selection 8.1 Advantages of GS 8.2 Disadvantages of GS 9. Genomic Selection in Potato 9.1 Need of Genomic Selection 9.2 Considerations in Genomic Prediction 9.3 Application of Genomic Prediction in Potato 10. Conclusion 6. Omics Approaches in Potato 1. Introduction 2. Transcriptomics 2.1 Microarray Technology 2.2 Transcriptome Sequencing (RNA-sequencing) 3. Applications of Transcriptomics 3.1 Biotic Stress Resistance 3.2 Abiotic Stress Tolerance 3.3 Tuber Quality and Other Traits 4. MicroRNAs 5. Proteomics 5.1 Biotic Stress 5.2 Abiotic Stress 5.3 Quality and Other Traits 6. Metabolomics 6.1 Biotic Stress 6.2 Abiotic Stress 6.3 Quality and Other Traits 7. Ionomics 8. Multi-Omics System 9. Conclusion 7. Phenomics in Potato 1. Introduction 2. Phenomics 3. High-Throughput Phenotyping (HTP) Platforms 4. Application of HTP in Potato 4.1 Agronomic Traits 4.2 Crop Canopy 4.3 Biotic and Abiotic Stresses 4.4 Root Traits 4.5 Aeroponics Technology 5. Conclusion 8. Genome Editing (CRISPR/Cas) Technology in Potato 1. Introduction 2. CRISPR/Cas Genome Editing 2.1 Steps Involved in CRISPR/Cas Construct Designing 2.2 CRISPR-Cas Transformation Systems 2.3 Gene Knockout Mechanism 2.4 DNA-free Genome Editing 2.5 Virus-induced Genome Editing 2.6 Base Editing 3. Application of CRISPR/Cas in Potato Improvement 3.1 Biotic Stress 3.1.1 Targeting DNA Virus Genome 3.1.2 Targeting RNA Virus Genome 3.1.3 Targeting Host Gene 3.1.4 Multiplexing Approach 3.2 Abiotic Stress 3.3 Tuber Quality, Phenotype and Other Traits 4. CRISPR/Cas Challenges in Tetraploid Potato 5. Conclusion 9. Conventional True Potato Seed (TPS) to Diploid Hybrid Potato Technologies 1. Introduction 2. True Potato Seed (TPS) Technology 3. Potato Production from TPS 3.1 Seedling Transplant Method 3.2 Seedling Tuberlets Method 4. Adoption of TPS Technology: A Case Study in India 5. Diploid Hybrid (F1) Potato Technology 6. Strategies of Diploid Hybrid 6.1 Selection of Recipient Parent (Dihaploid/Diploid Clone) 6.2 Selection of the Sli Gene Donor Parent 6.3 Development of Homozygous Diploid Inbred Lines 6.4 Development of F1 Hybrid 7. Genomics in TPS Research 7.1 Apomixis 7.2 Arabidopsis Apomictic Seeds: A Lesson for TPS 7.2.1 Development of MiMe (Mitosis Instead of Meiosis) Mutant 7.2.2 Development of GEM (Genome Elimination Mutant) 7.2.3 Development of F1 Hybrid (MiMe × GEM) 7.3 Genome Editing in Diploid Hybrid Potato 8. Challenges in Diploid Hybrid Production 9. Conclusion 10. Pre-breeding Genomics in Somatic Hybridization 1. Plant Tissue Culture 2. Somatic Hybridization 3. Somatic Hybridization Strategies 3.1 Protoplast Isolation and Fusion 3.2 Characterization of Somatic Hybrids 4. Application of Somatic Hybrids 4.1 Establishment of In Vitro Conservation Protocol 4.2 Genetics 4.3 Molecular Markers and Breeding 4.4 Genomics 5. Development of Potato Somatic Hybrids 6. Conclusion 11. Potato Transgenics 1. Introduction 2. Gene Cloning 3. Genetic Transformation 3.1 Agrobacterium Tumefaciens-mediated Transformation 3.2 Gene Gun-mediated Transformation 4. Development of Potato Transgenics 4.1 Late Blight Resistance 4.1.1 RB Gene Transgenics 4.1.2 RNAi Transgenics 4.2 Virus Resistance 4.2.1 Tomato Leaf Curl New Delhi Virus-potato (ToLCNDV-Potato) 4.2.2 Potato Virus Y (PVY) 4.3 Bacterial Wilt Resistance 4.3.1 RNAi Transgenics 4.3.2 EBD Gene Transgenics 4.4 Chip Quality with Reduced Cold-induced Sweetening 4.5 Protein-rich Potato 4.6 Dwarf Plant Architecture 4.7 Other Traits 5. Conclusion Index About the Author