Molecular Marker Techniques: A Potential Approach of Crop Improvement

Preface
Acknowledgment
Contents
About the Editor
1: Molecular Markers for Harnessing Heterosis
1.1 Introduction
1.2 Unveiling the Genetics of Heterosis via Molecular Markers
1.3 Genetic Diversity Assessment and Heterotic Grouping Using Molecular Markers
1.4 Prediction of Heterosis Using Molecular Markers
1.5 Current Challenges and Future Prospects
1.6 Conclusions
References
2: Kompetitive Allele-Specific PCR (KASP): An Efficient High-Throughput Genotyping Platform and Its Applications in Crop Varie...
2.1 Introduction
2.2 Evolution of Plant Molecular Markers
2.3 Kompetitive Allele-Specific PCR (KASP)
2.3.1 Principles of the KASP Technique
2.3.2 Requirements of KASP Assay
2.3.2.1 Prerequisites of KASP Assay
2.3.2.2 Thermal Cycle Reaction Components of KASP Assay
2.3.2.3 Standard Thermal Cycle Reaction Conditions for KASP Assay
2.3.3 Operational Steps of KASP Genotyping Technique
2.3.4 Why Is KASP Technique Being Used?
2.3.5 Application Fields of KASP Technology in Crop Improvement
2.3.6 Present Status of Utilization of the KASP Technique in Crop Improvement
2.3.6.1 Wheat
2.3.6.2 Maize
2.3.6.3 Rice
2.3.6.4 Legume Crops
2.3.6.5 Horticultural Crops
2.3.7 Advantages of KASP Genotyping Technique
2.3.8 Bottleneck of KASP Genotyping Technique
2.3.9 Prospects of KASP Technology
2.4 Conclusions
References
3: Marker Assisted Recurrent Selection for Crop Improvement
3.1 Introduction
3.2 Principle of MARS
3.3 General Outline of Mars
3.3.1 Parental Choice
3.3.2 Population Development
3.3.3 Genotyping
3.3.4 Phenotyping
3.3.5 QTL Analysis
3.3.6 Recombination Cycles
3.4 Strategies of Marker-Assisted Recurrent Selection (MARS)
3.5 Cost Efficiency of Marker-Assisted Recurrent Selection (MARS)
3.5.1 Factors that Control MARS Efficiency
3.5.1.1 Population Size Submitted to Selection at Each Cycle
3.5.1.2 Use of Single Versus Flanking Markers
3.5.1.3 Pre-Flowering/Early Selection
3.5.1.4 Number of Generations per Year
3.5.1.5 Price of Marker Data Points
3.6 Software Package for MARS Analysis
3.7 Application of MARS in Different Crops
3.8 Conclusion
References
4: Concepts and Employment of Molecular Markers in Crop Breeding
4.1 Introduction
4.2 Molecular Markers
4.2.1 Classification of Molecular Markers
4.2.1.1 Restriction Fragment Length Polymorphism (RFLP)
4.2.1.2 Randomly Amplified Polymorphic DNA (RAPD)
4.2.1.3 Simple Sequence Repeats (SSRs)
4.2.1.4 Amplified Fragment Length Polymorphism (AFLP)
4.2.1.5 Single-Nucleotide Polymorphism (SNP)
4.3 Employment of Molecular Markers in Crop Breeding
4.3.1 Determination of Genetic Diversity
4.3.2 Linkage Map Construction
4.3.3 QTL Mapping
4.3.4 Marker-Assisted Selection (MAS)
4.3.5 Association Mapping
4.3.6 Evolution and Phylogenic Study
4.3.7 Detection of Heterosis
4.3.8 Identification of Haploids
4.3.9 Genome-Wide Association Study (GWAS)
4.3.10 Marker-Assisted Backcrossing (MABC)
4.3.11 Marker-Assisted Gene Pyramiding
4.3.12 Targeting Induced Local Lesions in Genome (TILLING)
4.3.13 Genome Editing (CRISPR-Cas)
4.4 Conclusions
References
Untitled
5: Microsatellites as Potential Molecular Markers for Genetic Diversity Analysis in Plants
5.1 Introduction
5.2 Biodiversity
5.3 Analysis of Genetic Diversity
5.4 Molecular Markers
5.5 SSR (Simple Sequence Repeat) Markers
5.6 Types of SSR Markers
5.6.1 Genomic SSR Markers
5.6.2 EST-SSR Markers
5.7 ISSR (Inter-Simple Sequence Repeat) Markers
5.8 miRNA-Derived SSRs
5.9 Analysis Using SSR Markers
5.10 Use of Next-Generation Sequencing in Developing SSR Markers
5.11 SSR Markers in Characterization of Genetic Diversity
5.12 SSR Markers and Their Cross-Species Transferability
5.13 Conclusion
References
6: Application of Molecular Markers in Assessment of Genetic Diversity of Medicinal Plants
6.1 Introduction
6.2 Genetic Diversity
6.3 Methods for Assessing Genetic Diversity in Medicinal Plants
6.3.1 Morphological Markers
6.3.2 Cytological Markers
6.3.3 Biochemical Markers
6.4 Molecular Markers
6.4.1 Hybridization-Based Markers
6.4.2 PCR-Based Markers
6.4.2.1 Randomly Amplified Polymorphic DNA
6.4.2.2 Amplified Fragment Length Polymorphism
6.4.2.3 Microsatellite Markers
6.4.2.4 Inter Simple Sequence Repeats
6.4.2.5 Sequence-Related Amplified Polymorphism
6.4.2.6 Cleaved Amplified Polymorphic Sequences
6.4.2.7 Single Nucleotide Polymorphism
6.4.2.8 Diversity Arrays Technology
6.4.2.9 Sequence-Characterized Amplified Region
6.4.2.10 Start Codon Targeted Markers
6.4.2.11 Random Amplified Microsatellite Polymorphisms
6.4.2.12 Selective Amplification of Microsatellite Polymorphic Loci
6.4.2.13 DNA Amplification Fingerprinting
6.4.2.14 Directed Amplification of Minisatellite Region DNA
6.5 Diversity Assessment Works in Medicinal Plants
6.6 Conclusion
References
7: Non-coding RNA Based Marker: A New Weapon in Armory of Molecular Markers
7.1 Introduction
7.1.1 Detection of LncSSRs
7.1.2 Distribution in Genome
7.1.3 Development of LncRNA-SSRs Markers
7.1.4 Databases/Tools for LncRNA
7.2 Challenges and Future Prospects
7.3 Conclusion
References
8: Molecular Marker Techniques in Niger Crop Improvement
8.1 Introduction
8.2 Botanical Description
8.3 Genetic Problems in Niger Crop Improvement
8.4 Molecular Markers
8.4.1 Characteristics of a Good Molecular Marker
8.4.2 Types of Molecular Markers
8.4.3 Applications of Molecular Markers
8.5 Application of Molecular Markers in Niger Crop Improvement
8.5.1 Genetic Diversity
8.5.1.1 Random Amplified Polymorphic DNA Marker (RAPD)
8.5.1.2 ISSR Markers
8.5.1.3 Amplified Fragment Length Polymorphism (AFLP)
8.5.1.4 RAPD and AFLP
8.5.1.5 Simple Sequence Repeat (SSR) or Microsatellite Markers
8.5.1.6 Single Nucleotide Polymorphism (SNP)
8.5.1.7 Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNP)
8.5.1.8 Expressed Sequence Tags (ESTs)
8.5.1.9 Internal Transcribed Spacers (ITS)
8.5.2 Biological Processes and Abiotic Stresses
8.5.2.1 Micro RNAs
8.6 Conclusion
References
9: Applicability of Molecular Markers in Ascertaining Genetic Diversity and Relationship Between Five Edible Bamboos of North-...
9.1 Introduction
9.2 Materials and Methods
9.2.1 Sample Collection and DNA Extraction
9.2.2 PCR Amplification Reaction with ISSR, SCoT, CBDP, and iPBS Primers
9.2.3 Data Analysis
9.3 Results and Discussion
9.3.1 Polymorphism and Markers Efficacy
9.3.2 Correlation Analysis
9.3.3 Genetic Distance and Cluster Analysis by UPGMA
9.3.4 Principal Coordinate Analysis (PCoA)
9.4 Conclusion
References
10: DNA Markers-Assisted Crop Improvement for Biotic and Abiotic Stresses in Legumes
10.1 Introduction
10.2 DNA Markers
10.2.1 RFLP (Restriction Fragment Length Polymorphism)
10.2.2 RAPD (Randomly Amplified Polymorphic DNA)
10.2.3 AFLP (Amplified Fragment Length Polymorphism)
10.2.4 SSR (Simple Sequence Repeats)
10.2.5 ISSR (Intersimple Sequence Repeat)
10.2.6 STS (Sequence-Tagged Site)
10.2.7 CAPS (Cleaved Amplified Polymorphic Sequences)
10.2.8 SCARs (Sequence-Characterized Amplified Regions)
10.2.9 SNP (Single-Nucleotide Polymorphism)
10.2.10 GBS (Genotyping by Sequencing)
10.2.11 DArT (Diversity Array Technology)
10.3 DNA Markers-Assisted Characterization of Biotic Stress in Legumes
10.4 DNA Markers-Assisted Characterization of Abiotic Stress in Legumes
10.5 DNA Markers-Assisted Characterization of Stress-Related QTLs and Genes in Legumes
10.6 DNA Markers-Assisted Breeding and Development of Biotic Stress-Tolerant Lines in Legumes
10.7 Improvement of Legume Crops Via MAS
10.8 Amalgamation of Technologies with the Latest OMICS Approaches
10.9 Conclusion
References
11: Molecular Marker-Assisted Crop Improvement in Pulses
11.1 Introduction
11.2 Molecular Markers
11.3 Molecular Markers in Chickpea
11.4 Molecular Markers in Lentil
11.5 Molecular Markers in Fieldpea
11.6 Molecular Markers in Grass pea
11.7 Molecular Markers in Pigeonpea
11.8 Molecular Markers in Mungbean
11.9 Molecular Markers in Urdbean
11.10 Conclusion
References
12: Application of Molecular Markers for the Assessment of Genetic Fidelity of In Vitro Raised Plants: Current Status and Futu...
12.1 Introduction
12.2 Somaclonal Variation
12.2.1 Causes of Somaclonal Variation
12.2.2 Disadvantages of Somaclonal Variation
12.3 Detection of Somaclonal Variation Through Molecular Markers
12.3.1 Hybridization-Based Molecular Markers
12.3.1.1 RFLP
12.3.2 PCR-Based Molecular Markers
12.3.2.1 RAPD
12.3.2.2 AFLP
12.3.2.3 SCAR
12.3.2.4 ISSR
12.3.2.5 SSR
12.4 The Influence of Molecular Marker Techniques
12.5 Molecular Markers in the Age of Omics
12.6 Next-Generation Sequencing (NGS) for the Detection of Somaclonal Variation
12.7 Conclusion
References
13: Marker-Assisted Breeding in Vegetable Crops
13.1 Introduction
13.2 Classification of Markers
13.2.1 Morphological Markers
13.2.2 Biochemical Markers
13.2.3 Isozyme Markers
13.2.4 Seed Storage Proteins
13.2.5 Cytological Markers
13.2.6 Molecular Markers
13.3 Prerequisite of Marker-Assisted Selection (MAS)
13.3.1 Appropriate Marker Systems and Reliable Markers
13.3.2 Rapid DNA Extraction and High-Throughput Marker Detection
13.3.3 Genetic Map
13.3.4 Association Between Marker and Trait
13.4 Major Thrust Areas of Marker-Assisted Breeding
13.4.1 Marker-Assisted Backcrossing (MABC)
13.4.2 Marker Assisted Gene Pyramiding
13.4.3 Marker-Assisted Recurrent Selection (MARS)
13.4.4 Genomic Selection
13.5 Mapping Population
13.5.1 F2 Population
13.5.2 F2-Derived F3 Population
13.5.3 Backcross Population
13.5.4 Doubled Haploids
13.5.5 Recombinant Inbred Lines
13.5.6 Near-Isogenic Lines
13.6 Applications of Molecular Markers
13.6.1 Marker-Assisted Evaluation of Breeding Material
13.6.2 Marker-Assisted Backcrossing
13.6.3 Evolution and Phylogeny
13.6.4 Multitrait Introgression
13.6.5 Genetic Mapping
13.7 Genetic Enhancement of Vegetable Crops Using MAS
13.7.1 Tomato (Solanum lycopersicum L.)
13.7.2 Genetic and Genomic Resources
13.7.3 Mapped Genes and QTLs
13.7.4 Genomic and Marker-Assisted Selection
13.7.5 Pepper
13.7.6 Genetic and Genomic Resources
13.7.7 Mapped Genes and QTLs
13.7.8 Genomic and Marker-Assisted Selection
13.7.9 Brinjal
13.7.10 Genetic Resources
13.7.11 Mapped Genes and QTLs
13.7.12 Genomic and Marker-Assisted Selection
13.7.13 Pea
13.7.14 Genetic Resources
13.7.15 Mapped Genes and QTLs
13.7.16 Genomic and Marker-Assisted Selection
13.7.17 French Bean
13.7.18 Genetic Resources
13.7.19 Mapped Genes and QTLs
13.7.20 Genomic and Marker-Assisted Selection
13.7.21 Carrot
13.7.22 Genetic Resources
13.7.23 Mapped Genes/QTLs
13.7.24 Genomic and Marker-Assisted Selection
13.7.25 Cucumber
13.7.26 Genetic Resources
13.7.27 Mapped Genes and QTLs and Marker-Assisted Selection
13.7.28 Spinach
13.7.29 Genetic Resources
13.7.30 Mapped Genes and QTLs
13.7.31 Genomic and Marker-Assisted Selection
13.7.32 Okra
13.7.33 Genetic Resources
13.7.34 Mapped Genes/QTLs and Marker-Assisted Selection
13.8 Conclusion
References
14: Marker-Assisted Breeding for Soybean Mosaic Virus Resistance in Soybean (Glycine max)
14.1 Introduction
14.2 A Brief Summary of Soybean Mosaic Virus and Its Management
14.3 Nature of SMV Resistance
14.4 Marker-Assisted Breeding (MAB)
14.5 Synopsis of DNA Markers in Soybean
14.6 MAB for SMV Resistance
14.6.1 Mapping of SMV Resistance Genes
14.6.2 Genomic Regions and Candidate Genes Linked to SMV Resistance
14.6.2.1 Rsv Series
14.6.2.2 Rsc Series
14.6.2.3 QTLs and SNPs Associated with Resistance to SMV
14.6.3 Gene Pyramiding for SMV Resistance
14.7 Conclusion and Perspectives
References
15: Recent Advancements in Molecular Marker Technologies and Their Applications in Crop Improvement
15.1 Introduction
15.2 Molecular Markers
15.3 Molecular Markers for Crop Improvement
15.3.1 Restriction Fragment Length Polymorphism (RFLP)
15.3.2 Randomly Amplified Polymorphic DNA (RAPD)
15.3.3 Inter Simple Sequence Repeats (ISSR)
15.3.4 SSR
15.3.5 AFLP
15.3.6 SCAR
15.3.7 STS
15.3.8 CAPS
15.3.9 EST
15.3.10 SNP
15.3.11 DArT
15.3.12 SCoT
15.3.13 GBS
15.3.14 WGRS
15.4 Applications of Molecular Markers in Crop Improvement
15.4.1 Marker Assisted Selection (MAS)
15.4.1.1 Limitations of MAS
15.4.1.2 Marker-assisted Back-Cross Breeding
15.4.2 QTL Mapping
15.4.3 Gene Tagging
15.4.3.1 Tagging of Disease Resistance Genes
15.4.3.2 Tagging of Male Sterility Genes and Heterosis
15.4.4 Diversity Evaluation
15.4.5 Testing of Seed Purity
15.4.6 Gene Pyramiding
15.4.7 Map-Based Cloning of Genes
15.5 Conclusion
References
16: Recent Advances in the Use of Molecular Markers for Fruit Crop Improvement
16.1 Introduction
16.2 Types of Markers
16.2.1 Classical Markers
16.2.1.1 Morphological Markers
16.2.1.2 Cytological Markers
16.2.1.3 Biochemical Markers
16.2.1.4 DNA Markers
Restriction Fragment Length Polymorphism (RFLP)
PCR-Based Methods
16.3 Use of Molecular Markers in Fruit Crops
16.3.1 Estimation of Genetic Diversity
16.3.2 DNA Fingerprinting
16.3.3 Diagnosis of Diseases
16.3.4 Selection of Seedless Progenies
16.3.5 Determination of Sex in Fruit Crops
16.3.6 Linkage Maps and QTL Mapping in Fruit Crops
16.3.6.1 Association Mapping
16.3.7 Marker-Assisted Selection
16.4 Conclusion
References
17: Genomics-Assisted Breeding for Climate-Resilient Crops
17.1 Introduction
17.2 Genomics-Assisted Breeding for Climate-Resilient Crops
17.3 Genomics-Assisted Breeding: A Way Forward
17.3.1 Utilization of Crop Germplasm Resources (Genetic Resources) for Crop Genetic Improvement
17.3.2 Genome Sequencing and Sequence-Based Markers
17.3.3 High-Throughput Phenotyping
17.3.4 Marker-Trait Association for Genomics Assisted Breeding
17.3.5 Marker-Trait Association for Genomics-Assisted Breeding
17.4 Genomics Assisted Breeding for Stress Tolerance
17.4.1 Biotic Stress
17.4.2 Abiotic Stress
17.5 Genomics Assisted Breeding for Designing Future Crops
17.5.1 Haplotype-Based Breeding (HBB)
17.5.2 Accelerating Crop Breeding Development Through the Integration of High Throughput Phenotyping and Genomic Assisted Bree...
17.6 Conclusion
References