Advanced Crop Improvement, Volume 2: Case Studies of Economically Important Crops

As per the reports of FAO, the human population will rise to 9 billion by the end of 2050 and 70% of more food must be produced over the next three decades to feed the additional population. The breeding approaches for crop improvement programs are dependent on the availability and accessibility of genetic variation, either spontaneous or induced by the mutagens. Plant breeders, agronomists, and geneticists are under constant pressure to expand food production by employing innovative breeding strategies to enhance yield, adaptability, nutrition, resistance to biotic and abiotic stresses. In conventional breeding approaches, introgression of genes in crop varieties is laborious and time-consuming. Nowadays, new innovative plant breeding techniques such as molecular breeding and plant biotechnology, supplement the traditional breeding approaches to achieve the desired goals of enhanced food production. With the advent of recent molecular tools like genomics, transgenics, molecular marker-assisted back-crossing, TILLING, Eco-TILLING, gene editing, CRISPR CAS, non-targeted protein abundant comparative proteomics, genome wide association studies have made possible mapping of important QTLs, insertion of transgenes, reduction of linkage drags, and manipulation of genome. In general, conventional and modern plant breeding approaches would be strategically ideal for developing new elite crop varieties to meet the feeding requirement of the increasing world population. This book highlights the latest progress in the field of plant breeding, and their applicability in crop improvement. The basic concept of this 2-volume work is to assess the use of modern breeding strategies in supplementing the conventional breeding toward the development of elite crop varieties, for obtaining desired goals of food production. Preface Acknowledgments About the Book Contents About the Editors Plant Genetic Resources: Conservation, Evaluation and Utilization in Plant Breeding 1 Introduction 2 Genetic Diversity and Plant Genetic Resources 3 Conservation, Evaluation and Enhancement of PGRs 4 Conservation of Plant Genetic Resources Through Various Techniques 4.1 In Situ Conservation (Natural Ecosystem) 4.1.1 Genetic Reserve Conservation 4.1.2 On-Farm Conservation 4.2 Ex Situ Conservation 4.2.1 Seed Storage Conservation 4.2.2 In Vitro Conservation 4.2.3 Slow Growth 4.2.4 Cryopreservation 4.2.5 Pollen Conservation 4.2.6 Field Gene Bank Conservation 4.2.7 Botanical Garden Conservation 4.2.8 Plant Herbarium 5 Role of Biotechnology in the Conservation of Plant Genetic Resources 5.1 Cryopreservation 5.2 Development of Pathogen-Free Planting Material 5.3 Removal of Sexual Barrier for Germplasm Uses 5.4 Characterization of Genetic Diversity 5.5 DNA Bank or Preservation of DNA 6 Major Centres for Conservation and Maintenance of Plant Genetic Resources of Various Crops in India and the World 7 Status of Germplasm of Different Crops at Indira Gandhi Krishi Vishwavidyalaya, (IGKV), Raipur, India 7.1 Status of Rice Germplasm at IGKV, Raipur 7.2 Status of Grass Pea Germplasm at IGKV, Raipur, India 7.3 Status of Linseed Germplasm at IGKV, Raipur, India 7.4 Pigeonpea 7.5 Chickpea 7.6 Medicinal Plants 8 Strategies for Conservation of Huge Rice Germplasm Collection at IGKV, Raipur, India 8.1 On-Farm Conservation of Rice Germplasm at IGKV, Raipur 8.2 Package of Practices Followed for Obtaining a Healthy Crop in On-Farm Conservation 8.3 Medium-Term Storage Facilities at IGKV, Raipur 9 Characterization, Evaluation, Cataloguing and Documentation of PGRs 9.1 Characterization 9.1.1 Morphological Characterization 9.1.2 Biochemical Characterization 9.1.3 Molecular Characterization 9.2 Evaluation 9.3 Descriptors 9.3.1 Characterization Descriptors 9.3.2 Botanical Taxonomic Descriptors 9.3.3 Morpho-Agronomic Descriptors 9.3.4 Evaluation Descriptors 9.4 Documentation and Cataloguing of PGRs 9.4.1 EURISCO (European Search Catalogue for Plant Genetic Resources) 9.4.2 EAPGREN (The Eastern Africa Plant Genetic Resources Network) 9.4.3 GRIN Global (Germplasm Resource Information Network Global) 9.5 Cataloguing of PGRs at Various National and International Organizations 9.5.1 National Organizations 9.5.2 International Collaborations 10 Utilization of PGRs in Crop Improvement 10.1 Development of Core Set, Mini-core and Reference Sets 10.2 Development of Improved Varieties 10.2.1 Introgression 10.2.2 Incorporation 10.2.3 Pre-breeding 10.3 Development of Novel Crop 10.4 Climate Resilience 10.5 Resistance to Biotic Stress 10.6 Apomixis 10.7 Biofortification 10.8 Pharmaceutical Industries 11 Major Problems Associated with the Conservation, Evaluation and Enhancement of PGRs 11.1 Population Growth and Deforestation 11.2 Varietal Modernization 11.3 Climate Change 11.4 Genetic Erosion 11.5 Genetic Vulnerability 11.6 Lack of Technical Knowledge 12 Way Ahead 13 Conclusion References SINE Markers as a Powerful Tool for Assessing Genetic Diversity to Improve Potato 1 Introduction 2 Retrotransposon-Based Marker Systems Are Well Suited to Assess Genetic Diversity 3 SINE Retrotransposons Are Informative Molecular Markers for Plant Breeding 4 SINEs Can Be Identified from Available Sequence Data 5 Genetic Fingerprinting Applying the Inter-SINE Amplified Polymorphism (ISAP) Marker System 6 Phenotyping Bulgarian Potato Variety and Mutant Lines from the MVCRI Collection 7 Morphological Characteristics of Potato Mutant Lines in the Maritsa VCRI Collection 8 Genotyping of Bulgarian Potato Variety by Using ISAP Molecular Reactions 9 Genotyping Bulgarian Mutant Lines Using ISAP Molecular Technique: Case Study 9.1 Material and Methods 9.2 Molecular Method 9.3 Statistical Method 9.4 Results and Discussion 10 Conclusions References Applicability of ISAP and RAPD Techniques for Capsicum Collection Genotyping 1 Introduction 1.1 Molecular Marker Systems 1.2 RAPD for Pepper Genotyping 1.3 Application of RAPD for Pepper Characterization 1.4 Microsatellite Analysis in Pepper 1.5 Mobile Genetic Elements as a Base for Molecular Marker Systems 1.6 Applicability of Potato-Derived ISAP for Pepper Genome Characterization 1.6.1 Materials and Methods Plant Material 1.6.2 Molecular Methods Data Analysis 1.6.3 Results Results of ISAPInter-SINE Amplified Polymorphism (ISAP) Reactions Performed with a Forward and a Reverse Primer Designed from Different Sol-SINE Families ISAP Reactions Performed with Primers Designed from Three and More Sol-SINE Families ISAP Single-Family Reactions Performed with Primers Designed from the Same Sol-SINE Family 1.6.4 Discussion 1.6.5 Conclusions References Improved Breeding of High-Carotene Carrots Through Marker-Assisted Paternity Selection and Raman Spectroscopy 1 Introduction 1.1 Breeding for Pigments in Carrots 1.2 Polycrossing 2 Materials and Methods 2.1 Plant Material 2.2 DNA Extraction 2.3 Microsatellite Assay 2.4 Data Treatment and Paternity Analysis 3 Results 3.1 Single Sequence Repeat (SSR) Markers 3.2 Genetic Relationship Between Parent Cultivars 3.3 Parent Assignment 4 Discussion 5 Conclusion References Traditional and Modern Molecular Cytogenetic Approaches to the Study of Mutagen-Induced DNA Damage: A Case of Fagopyrum Species 1 Introduction 2 Material and Methods 2.1 Material 2.2 Mutagenic Treatment 2.3 Analyses of the Mitotic Index and the Micronuclei 2.4 TUNEL Test 3 Results 3.1 Plant Growth and Morphology 4 Cytological Analyses 4.1 Mitotic Activity 4.2 Micronuclei 4.3 DNA Damage 5 Discussion 6 Conclusion and Future Perspective References Improvement of Yield in Cowpea Varieties Using Different Breeding Approaches 1 Introduction 2 Hybridization 2.1 Interspecific Hybridization in the Subgenus Vigna 3 Tissue Culture 4 Mutation Breeding 5 Molecular Breeding 5.1 Biotic Stress Resistance 5.2 Abiotic Stress Resistance 5.3 Cowpea Genetic Maps and Trait-Linked Markers 5.4 Quality and Nutritional Traits 6 Conclusion References Germplasm Diversity and Breeding Approaches for Genetic Improvement of Mungbean 1 Introduction 1.1 Taxonomic Classification and Geographic Distribution 1.2 History, Origin, and Domestication 1.3 Cytogenetics 1.4 Nutritional Values and Importance 1.5 Adaptation and Cultivation 2 Production Statistics 3 Biotic and Abiotic Stress 4 Breeding Strategies and Constraints 5 Conclusion References Mutation Breeding for Adaptation to Climate Change in Seed Propagated Crops 1 Introduction 2 Impact of Climate Change on the Productivity of Seed Propagated Crops 3 Mutation Breeding for Adaptation to Climate Change 3.1 Mutations for Quantitative Traits 3.1.1 Yield and Yield Components Asia Europe North America Latin America Africa 3.1.2 Mutations for Early Maturity 3.1.3 Mutations for Improved Plant Architecture 3.2 Mutations for Abiotic Stresses 3.3 Mutations for Biotic Stresses 4 Strategies to Overcome the Negative Impact of Climate Change 5 Conclusion References Induced Mutagenesis-A Reliable Technology to Overcome the Limitations of Low Genetic Variability in Lentils 1 Introduction 2 Origin, Area, Production, and Productivity of Lentil 3 Nutrient Composition and Growth Habit of Lentil 4 Varieties, Climatic Conditions, Insect Pests, and Diseases of Lentil 5 Limitations and Scope of Traditional and Modern Plant Breeding 6 Mutagenesis in Lentil 6.1 Mutagenesis and Biological Damage 6.2 Cytological Effects 6.3 Chlorophyll and Morphological Mutations 6.4 Induced Variability for Quantitative Traits References Abiotic Stress Tolerance and Nutritional Improvement in Chickpeas Through Recombination, Mutation, and Molecular Breeding 1 Introducing Chickpeas 2 Abiotic Stresses and Impact on Chickpea Cultivation 3 Abiotic Stresses, Adaptive Mechanisms, and Target Traits in Chickpea 3.1 Low-Temperature Stress 3.2 High-Temperature (Heat) Stress 3.3 Drought Stress 3.4 Salinity Stress 3.5 Selection and Screening of Traits: Conventional Methods to Modern Tools 3.6 Breeding Approaches for Abiotic Stresses Tolerance and Some Success Stories 4 Developing Nutritionally Improved Chickpeas 5 Co-improving Stress Tolerance and Quality Parameters-Paradox or Possibility? 6 Conclusion and Future Prospects References Application of Molecular Markers on Assessing Genetic Diversity in Faba Bean 1 Introduction 2 Non-PCR-Based Markers 2.1 Restriction Fragment Length Polymorphism (RFLP) 3 PCR-Based Markers 3.1 Random Amplified Polymorphic DNA (RAPD) 3.2 Sequence-Specific Amplification Polymorphism (SSAP) 3.3 Amplified Fragment Length (AFLP) 3.4 Sequence-Related Amplified Polymorphism (SRAP) 3.5 Inter Simple Sequence Repeats (ISSRs) 3.6 Simple Sequence Repeat (SSR) 4 Sequence-Based Marker 4.1 Single Nucleotide Polymorphism (SNP) 4.2 Expressed Sequence Tags (EST)-SSR 5 Conclusions References Conventional and Molecular Breeding for Genetic Improvement of Maize (Zea mays L.) 1 Introduction 2 Conventional Breeding Approaches: Success and Limitations 2.1 Grain Yield 2.2 Biotic and Abiotic Stresses 2.3 Quality Traits 3 Molecular Breeding 3.1 QTL Mapping for Different Traits 3.1.1 Grain Yield 3.1.2 Biotic and Abiotic Stress 3.1.3 Quality Traits 3.2 Molecular Breeding-Based Trait Improvement: Achievements 4 Conclusion and Future Perspectives References Conventional and Molecular Breeding for Sunflower Nutrition Quality Improvement 1 Introduction 2 Specificities in Sunflower Breeding 3 Main Directions in Sunflower Breeding Related to Nutrition Quality 3.1 Classical Oil Type 3.2 Altered Oil Quality 3.3 Confectionery Sunflower 4 Genetic Resources for Oil Quality Improvement 4.1 Helianthus Genus – Crop Wild Relatives (CWR) 4.2 Local Populations, Open Pollinated Varieties, and Public Lines 4.3 Mutations 4.4 Genetic Stocks of Public Breeding Sector 5 Main Objectives in Sunflower Breeding for Nutritional Quality 5.1 Yield and Yield Related Traits 5.1.1 Molecular Tools 5.2 Oil Content and Quality Traits 5.2.1 Molecular Tools Oil Content Increased Oleic Acid Content Increased Stearic Acid Content Tocopherols 5.3 Abiotic Stress Tolerance and Nutrition Quality Traits 5.3.1 Molecular Tools 5.3.2 Genomic Selection for Sunflower Improvement 6 Future Breeding Challenges References Mendelian to Genomics and Bioinformatics Approaches in Cytoplasmic Male Sterility and Fertility Restoration in Sorghum Breeding 1 Introduction 2 Sorghum Area and Production 3 Constraints in Post-rainy Sorghum Hybrid Breeding 4 Cytoplasm Diversity in Sorghum 5 Cytoplasmic Male Sterility: Rf (Fertility Restoration) System 6 Molecular Basis: The Mitochondrial Route 7 Molecular Basis: The Nuclear Route 8 In Silico Analysis of Candidate Genes Encoding PPR Protein 9 Pentatricopeptide Repeat Protein (PPR) Family 10 Molecular Models for Mitochondrial-Nuclear Gene Interaction and Fertility Restoration 11 Cytotoxicity Model 12 Energy Deficiency Model 13 Programmed Cell Death Model (PCD) 14 Retrograde Regulation Model 15 Marker-Assisted Selections for Fertility Restoration Trait 16 Conclusions and Prospects References In Vitro Embryo Rescue Techniques and Applications in Hybrid Plant Development 1 Introduction 2 Interspecific and Intergeneric Hybridization: Associated Constraints 2.1 Interspecific and Intergeneric Hybrid Failures: Main Causes 2.1.1 Effects of Precocious Seed Germination 2.1.2 Influence of Nutritional Starvation on Embryo Development 2.1.3 Implications of Cytological Aberrations in Embryogenesis 2.1.4 Biological Significance of the Endosperm Balance Number 2.1.5 Importance of the Polar-Nuclei Activation Hypothesis 2.1.6 Effects of Pre- or Post-Zygotic Barriers on Endosperm Development 3 Embryo Rescue Techniques and Essence of Application 3.1 Historical Notes on the Embryo Rescue and Culture Technology 3.2 Types of Embryo Culture Technique 3.2.1 Mature Embryo Culture 3.2.2 Immature Embryo Culture 3.3 Factors That Influence the Success of Embryo Culture 3.3.1 Genotypic Background of Embryo 3.3.2 Developmental Stage of the Isolated Embryo 3.3.3 Composition of the Nutrient Media 3.3.4 Growth Temperature and Light Conditions 3.4 Salient Considerations Involved in Embryo Rescue and Culture 3.4.1 Determination of Appropriate Embryo Stage for Rescue 3.4.2 Embryo Excision Techniques 3.4.3 Media Manipulations for Efficient Embryo Culture 3.5 Major Embryo Rescue and Culture Procedures 3.5.1 Rescue and Culture of Embryos 3.5.2 Embryo-Nurse Endosperm Transplant Method 3.5.3 In Vitro Ovary Culture 3.5.4 Ovule Culture Technique 3.5.5 Ovary and Ovule Slice or Perforation Procedure 3.6 Applications of the Embryo Rescue Technique 3.6.1 Overcoming Seed Dormancy 3.6.2 Shortening of the Breeding Cycle in Plants 3.6.3 Overcoming Embryo Abortion 3.6.4 Development of Plants in Seedless Varieties 3.6.5 In Vitro Vegetative Propagation of Plants 3.6.6 Germplasm Conservation: Preservation of Embryos and Regrowth 3.6.7 Homozygous Monoploid Production 4 Conclusion References Proteomic and Biochemical Research for Exploring the Role of Plant-Derived Smoke in Food Crops 1 Introduction 2 Chemistry of Plant-Derived Smoke Solution 3 Morphological and Physiological Responses of Plants to Plant-Derived Smoke Solution 3.1 Seed Germination 3.2 Plant Growth 4 Biochemical Responses of Plants to Plant-Derived Smoke Solution 4.1 Photosynthesis 4.2 Phenol and Flavonoids 4.3 Other Biochemical Changes 5 Molecular Responses of Plants to Plant-Derived Smoke Solution 5.1 Plant-Derived Smoke 5.2 Karrikins 6 Concluding Remarks References Genome-Wide Association Study (GWAS): Concept and Methodology for Gene Mapping in Plants 1 Introduction 2 History of GWAS 3 Principle and Basic Procedure for Conducting GWAS in Plants 3.1 Linkage Disequilibrium 3.2 Linkage Disequilibrium Decay 3.3 Steps in GWAS Analysis 3.3.1 Selection of Diverse Panel of Individuals 3.3.2 Phenotyping of the Association Panel for the Trait of Interest 3.3.3 Genotyping of the GWAS Association Panel 3.3.4 Population Structure Analysis Based on the Genotyping Information 3.3.5 Marker-Trait Association Analysis 4 Data Generation and Quality Filtrating for GWAS 4.1 Genotypic Data 4.2 Phenotypic Data 4.3 Quality Control 4.3.1 Outlier Detection 4.3.2 Data Normality 4.3.3 Imputation Quality 4.3.4 Missing Data 4.3.5 Minor Allele Frequency 4.3.6 Linkage Disequilibrium (LD) Pruning 4.3.7 Hardy-Weinberg’s Equilibrium (HWE) 4.3.8 Marker Heterozygosity 5 Statistical Models for GWAS 5.1 Single-Locus Models 5.1.1 ANOVA: Analysis of Variance 5.1.2 GLM: General Linear Model 5.1.3 MLM: Mixed Linear Model 5.1.4 CMLM: Compressed MLM 5.1.5 ECMLM: Enriched Compressed MLM 5.1.6 SUPER: Settlement of MLM Under Progressively Exclusive Relationship 5.1.7 EMMA: Efficient Mixed-Model Association 5.1.8 GEMMA: Genome-Wide Efficient Mixed-Model Association 5.1.9 FaST-LMM: Factored Spectrally Transformed Linear Mixed Models 5.2 Multi-locus Models 5.2.1 MLMM: Multiple Loci MLM 5.2.2 FarmCPU: Fixed and Random Model Circulating Probability Unification 5.2.3 mrMLM: Multi-locus Random-SNP-Effect MLM 5.2.4 FASTmrMLM: Fast Multi-locus Random-SNP-Effect MLM 5.2.5 FASTmrEMMA: Fast Multi-locus Random-SNP-Effect EMMA 5.3 Multi-trait Models 5.4 Multi-locus, Multi-trait Models 6 Multiple Hypothesis Testing in GWAS 7 Databases and Tools for GWAS 7.1 Databases for GWAS 7.1.1 GWAS Atlas 7.1.2 GrainGenes 7.1.3 Triticeae Toolbox 7.1.4 Pea Marker Database (PMD) 7.1.5 NABIC Marker Database 7.2 Tools for GWAS Data Analysis 7.2.1 PLINK 7.2.2 GAPIT 7.2.3 STRUCTURE 7.2.4 TASSEL 7.2.5 GWASpro 7.2.6 METAL 7.2.7 GWAMA: Genome-Wide Association Meta-analysis 7.3 R-Packages for GWAS 8 Prioritization of Associated Genomic Regions/Prediction of Candidate Genes 9 Limitations of GWAS 9.1 False-Negative/False-Positive Results During Multiple Testing 9.2 Missing Heritability 9.3 Heritability of Complex Traits 9.4 Genetic Heterogeneity 9.5 Synthetic Associations/Misleading Associations 10 GWAS Studies in Plants 11 Integration of GWAS and QTL Mapping for Fine Mapping and Candidate Gene Discovery of Complex Trait 12 Integration of “Omics” Data in GWAS 13 Conclusion and Prospects References Tweaking CRISPR/Cas for Developing Salt and Drought Tolerant Crop Plants 1 Introduction 2 Molecular Breeding Approaches for Drought- and Salt-Tolerant Crop Plants 3 Genome Editing Strategies Crop Improvement 4 CRISPR for Developing Abiotic Stress Tolerance in Crop Plants 5 CRISPR/Cas Genome Editing for Plant Tolerance to Drought Stress 6 CRISPR/Cas Genome Editing for Plant Tolerance to Salinity 7 Conclusion and Future Directions References CRISPR/Cas in Improvement of Food Crops for Feeding the World into the Future 1 Introduction 2 Need for Crop Improvement 3 Genome-Editing Technology Over Conventional Genetic Modification in Crop Improvement 4 CRISPR/Cas as a Tool to Feed the World into the Future 5 Progress of CRISPR in Crop Improvement 5.1 Vegetables 5.1.1 Quality Improvement 5.1.2 Biotic and Abiotic Stress 5.1.3 Others 5.2 Cereals 5.2.1 Quality Improvement 5.2.2 Biotic and Abiotic Stress 5.3 Fruits 5.3.1 Quality Improvement 5.3.2 Biotic and Abiotic Stress 5.4 Pulses 5.5 Seeds and Nuts 5.5.1 Quality Improvement 5.5.2 Biotic and Abiotic Stress 5.6 Herbs and Spices 6 Limitations in CRISPR/Cas 6.1 Global Regulatory Bodies for CRISPR-Edited Crops 6.2 Bioethics and Risk Assessment 7 Challenges and Future Prospect 8 Conclusion References Index