Text Book on Molecular Marker Technology

A Text Book on Molecular Marker Technology for Crop Improvement

N. Manikanda Boopathi

M. Raveendran

Table of Contents

1. Genome Organization

1.1 Genome Structure and Complexities

1.2 Methods of Genome Analysis

1.3 Need for understanding genome structure and function

2. Evolution of Different Kinds of Markers

2.1 Role of markers in genome analysis

2.2 Morphological markers

2.3 Biochemical markers

2.4 Molecular markers

2.5 Historical perspectives of different kinds of markers, advantages and limitations

3. Early Generation Molecular Markers

3.1 Classification of molecular markers

3.2 RFLP

3.3 RAPD

3.4 AFLP

3.5 SSR and ISSR

3.6 SCAR

3.7 STS

3.8 Transferability of Markers across the Genera

4. Next Generation Molecular Markers

4.1 SNP

4.1.1 Whole Genome Marker Discovery

4.1.2 Methods in SNP Discovery

4.2 DArT

4.3 InDels

4.4 CNV and PAV

5. Genome Mapping

5.1 Genetic Mapping

5.1.1 Principles of Genetic Mapping

5.1.2 Development of Mapping Population

5.1.2.1 DH lines

5.1.2.2 F₂ progenies

5.1.2.3 RILs

5.1.2.4 BC progenies

5.1.2.5 NILs

5.1.2.6 Four-way mapping populations

5.1.2.7 NAM population

5.1.2.8 MAGIC population

5.1.2.9 Pseudo Test Cross in Fruit Crops

5.1.2.10 Natural populations for GWAS

5.1.3 Process of Genetic Mapping

5.1.3.1 Mapping Functions

5.2 Physical Mapping

5.2.1 Methods in Physical Mapping

5.2.2 Second and Third generation sequencing

5.2.3 Genome assembly and Chromosomal Assignment

6 QTL Mapping

6.1 Principle of QTL mapping

6.2 Single Marker Analysis

6.3 Interval Mapping

6.4 Composite Interval Mapping

6.5 Association Mapping

6.6 AB-QTL Analysis

6.7 Major Genes and Minor Genes

6.8 Advances in QTL Mapping

6.8.1 Comparative Genome Mapping

6.8.2 Integration of Genetic and Physical Maps

6.8.3 Fine Mapping

6.8.4 Map Based Cloning

6.9 Precautions in QTL mapping for MAS

6.9.1 Selection of QTLs for MAS

6.9.2 Identification of Gene Specific Markers

6.10 Linking QTL and Omics data: Genomics Assisted Breeding

7. Applications of Molecular Markers

7.1 Allele Mining

7.2 Characterization of Plant Genetic Resources

7.3 Genetic Diversity Analysis

7.4 Plant Variety Protection and Molecular Markers

7.4.1 DNA Fingerprinting

7.5 Varietal and Hybrid Purity testing

7.6 Testing of true-to-type plants produced through Micropropagation

7.7 Marker Assisted Breeding

7.7.1 MAS: Principle and Method

7.7.1.1 Foreground, Background and Recombinant Markers

7.7.2 MABC: Principle and Method

7.7.2.1 Marker Assisted Pyramiding

7.7.3 MARS: Principle and Method

7.7.4 GS: Principle and Method

8. Molecular Plant Breeding

8.1 Traditional Plant Breeding

8.1.1 Aims and Principles of Plant Breeding

8.1.2 Conventional Breeding Methods for Self- and Cross-Pollinated Crops

8.1.3 Limitations of Conventional Breeding Strategies

8.1.4 Role of Molecular Breeding in Crop Improvement

8.2 Molecular Plant Breeding

8.2.1 Traits that are suitable for Molecular Breeding

8.2.2 Selection of Markers

8.2.3 Selection of Appropriate Molecular Breeding Strategies

8.2.4 Transgenic Breeding

9. Molecular Markers and Rice

9.1 Improvement of Biotic Stress Resistance

9.2 Improvement of Abiotic Stress Resistance

9.3 Nutritional Quality improvement

9.4 Future perspectives

10. Molecular Markers and Maize

10.1 Improvement of Biotic Stress Resistance

10.2 Improvement of Abiotic Stress Resistance

10.3 Nutritional Quality improvement

10.4 Future perspectives

11. Molecular Markers and Wheat

11.1 Improvement of Biotic Stress Resistance

11.2 Improvement of Abiotic Stress Resistance

11.3 Nutritional Quality improvement

11.4 Future perspectives

12. Molecular Markers in Other Field Crops

12.1 Success Stories

12.2 Future Perspectives

13. Molecular Markers and Vegetables

13.1 Vegetables and their importance

13.2 Conventional Methods for Vegetable Crop Improvement

13.3 Molecular Markers and Vegetables

13.4 Improvement of Biotic Stress Resistance

13.5 Improvement of Abiotic Stress Resistance

13.6 Nutritional and Other Quality improvement

13.7 Future perspectives

14. Molecular Markers and Fruit Crops

14.1 Fruit Crops and their importance

14.2 Conventional Methods for Fruit Crops Improvement

14.3 Molecular Markers and Fruit Crops

14.4 Improvement of Biotic Stress Resistance

14.5 Improvement of Abiotic Stress Resistance

14.6 Nutritional and Other Quality improvement

14.7 Future perspectives

15. Molecular Markers and Spices, Plantations and Ornamental Flower Plants

15.1 Spices

15.2 Plantation Crops

15.3 Ornamental Flower Plants

15.4 Molecular Markers and their applications

16. Molecular Markers and Forest Trees

16.1 Forest Trees and Their Importance

16.2 Conventional Breeding Methods in Forest Trees

16.3 Applications of Molecular Markers in Forest Trees