QTL Mapping in Crop Improvement: Present Progress and Future Perspectives

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QTL Mapping in Crop Improvement: Present Progress and Future Perspectives
Copyright
Contents
Contributors
Chapter 1: Recent advances in molecular marker technology for QTL mapping in plants
1. Introduction
2. Advances in marker developments
2.1. Sequence-based markers
2.2. Next-generation molecular marker technologies
3. Trait associations and QTL mapping
3.1. Mapping populations
3.2. Statistical tools used in QTL mapping
3.3. Bulk segregant analysis: Rapid approach for quantitative trait mapping
3.4. Advanced approaches for QTL mapping
3.5. QTL mapping using high-throughput marker genotyping
4. Conclusion
References
Chapter 2: A statistical perspective of gene set analysis with trait-specific QTL in molecular crop breeding
1. Background
2. Structure of gene set analysis
2.1. Units of gene set analysis
2.2. Hypotheses in gene set analysis
2.3. Sampling models in gene set analysis
2.3.1. Subject sampling model
2.3.2. Gene sampling model
3. GSA approaches for high-throughput GE studies
4. Statistical approach for gene set analysis with QTLs
4.1. Illustration of performance of the GSAQ approach
4.2. Distribution of NQhits statistic
4.3. Gene sets analysis with QTLs
4.4. Performance analysis of gene set selection methods based on GSAQ
5. Statistical perspectives of GSAQ
6. Limitations and future challenges of GSA
6.1. Biological annotation challenges
6.2. Methodological challenges
Acknowledgment
References
Chapter 3: Crop improvement againstColletotrichum truncatum using molecular breeding approaches
1. Introduction
2. Genus Colletotrichum
3. The biotrophy-necrotrophy switch
4. Colletotrichum truncatum
4.1. Infection mode
4.2. Genome
4.3. Host specificity
4.4. Molecular basis for host-pathogen interaction
4.5. Genetics and genomics of host plant resistance
5. Soybean anthracnose
6. Conclusion and future prospects
References
Chapter 4: Molecular breeding for drought and heat stress in maize: Revisiting the progress and achievements
1. Introduction
2. Effects of drought and heat stress and plant response
3. Molecular breeding
3.1. QTL mapping: Approach and progress
3.1.1. Drought stress tolerance
3.1.2. Heat stress tolerance
3.2. Genome wide association studies/association mapping
3.3. Genomic selection
4. Conclusion and future perspectives
References
Chapter 5: Molecular breeding for improving yield in maize: Recent advances and future perspectives
1. Introduction
2. Molecular breeding
3. Why to use MB?
4. Molecular breeding for grain yield: Key considerations
5. Molecular breeding for yield improvement: Broad outlines
6. Molecular breeding schemes
6.1. Marker-assisted backcross breeding
6.1.1. Selection for gene/QTL of interest
6.1.2. Minimizing linkage drag
6.1.3. Selection for the RP
6.2. Marker-assisted forward breeding
6.3. Marker-assisted gene pyramiding
6.3.1. Sequential approach
6.3.1.1. Sister line crossing
6.3.1.2. Step-wise backcrossing
6.3.2. Simultaneous/synchronized approach
6.3.3. Convergent backcrossing
6.4. Marker-assisted recurrent selection
6.5. Genomic selection or genome-wide selection
6.5.1. Factors affecting success of GS
6.6. Phenotype-integrated MAS
7. Perspectives
References
Chapter 6: Abiotic stress tolerance in wheat (Triticum aestivum L.): Molecular breeding perspectives
1. Introduction
2. Impact of abiotic stresses on wheat
2.1. Drought stress
2.2. Heat stress
2.3. Salinity stress
3. Genomic regions/QTL associated with abiotic stresses
3.1. QTL associated with drought stress
3.2. MetaQTL studies in wheat for drought stress
3.3. QTL associated with heat stress
3.4. QTL associated with salinity stress
4. Molecular breeding for abiotic stress tolerance
5. High-throughput genotyping platforms: Assist wheat molecular breeding
6. Speed breeding for accelerating plant breeding
7. Conclusions and future outlook
1IntroductionBread wheat (Triticum aestivum L.) is a key staple food crop globally and providing about 20% of the
References
Chapter 7: Advances in QTL mapping for biotic stress tolerance in wheat
1. Introduction
1.1. Wheat breeding
1.2. Resistance versus susceptible wheat breeding
2. Significant diseases and insect pests of wheat
2.1. Powdery mildew
2.2. Wheat blast
2.3. Tan spot
2.4. Septorias
2.5. Spot blotch
2.6. Fusarium head blight
2.7. Downy mildew (Sclerophthora macrospora (Sacc.))
2.8. Loose smut (Ustilago tritici (Pers.) Rostr.)
2.9. Flag smut (Urocystis agropyri)
2.10. Karnal bunt (Tilletia indica)
2.11. Common bunt (Tilletia tritici) and dwarf bunt (Tilletia controversa)
2.12. Root rots and nematodes
2.13. Viruses
2.14. Insects
2.15. Aphids
2.16. Cereal leaf beetle
2.17. Ghujia weevil
2.18. Termites
2.19. Pink stem borer
2.20. White grubs
3. QTL approach and its importance in biotic stress improvement in wheat
4. QTL mapping on diseases and pests of wheat
4.1. Fusarium head blight
4.2. Powdery mildew
4.3. Wheat blast
4.4. Loose smut
4.5. Karnal bunt
4.6. Flag smut
4.7. Insect pests
5. Conclusion and future perspectives
References
Chapter 8: Drought stress tolerance in wheat: Recent QTL mapping advances
1. Introduction: Global importance of wheat
2. Climate change effect on wheat
3. Physiology of wheat plant
4. Drought stress mechanism in wheat
5. Advances in molecular breeding techniques
6. Wheat QTL mapping for drought tolerance
References
Chapter 9: Wheat biofortification: A molecular breeding outlook
1. Introduction
2. Wheat grain components
2.1. Protein
2.2. Micronutrients
2.3. Pigments: Lutein, yellow pigments, and anthocyanin
2.4. Phytic acid
3. Strategies for combating hidden hunger
3.1. Food supplementation
3.2. Diversifying diet
3.3. Biofortification
4. Biofortification for GPC
4.1. GPCB1-Lone contributor of GPC
4.2. Identification of different sources of GPC
5. Biofortification for grain zinc content
5.1. Agronomic biofortification
5.2. Nano-fertilization
5.3. Exploitation of wild germplasm
5.4. QTLs mapped in seed for Zn content
5.5. Grain Zn content and transgenics
6. Biofortification for grain iron content
6.1. Localization of Fe in wheat
6.1.1. Conventional breeding
6.1.2. Transgenic approaches
6.1.3. Understanding gene regulation
6.1.4. Combinatorial approach
7. Biofortification for grain selenium content
7.1. Localization of Se in wheat
7.2. Variation for selenium accumulation in plants
7.2.1. Agronomic biofortification
7.2.2. Nano-fertilization
7.2.3. Genetic engineering
7.2.4. Exploiting the genetic variation
7.2.5. Conventional and molecular breeding approach
8. Phytic acid-Culprit for hidden hunger
9. Biofortification for pigments
9.1. Carotenoids
9.2. Anthocyanins
9.3. Flavonoids
9.4. Color variations in wheat grain
9.5. Molecular breeding strategies
9.6. Consumer preferences
9.7. Environmental effect on color accumulation
9.8. Recent progress in breeding of colored wheats
10. Conclusion
References
Further reading
Chapter 10: Identification of tolerance for wheat rusts: Insights in recent QTL mapping efforts
1. Introduction
2. Impact of biotic stresses on wheat production
3. Wheat rust diseases
4. Insects-pests affecting wheat
5. Viral diseases
6. Types of rusts attack on wheat and mode of action
7. Wheat stem rust
8. Wheat stripe rust
9. Wheat leaf rust
10. Conventional breeding and molecular techniques to control rusts attack
11. Stem rust resistance
12. Stripe rust resistance in wheat
13. Leaf rust resistance in wheat
14. QTL mapping for rusts attacks
15. Summary
References
Chapter 11: Abiotic and biotic stress tolerance in rice: Recent advances in molecular breeding approaches
1. Introduction
2. QTL mapping approaches
2.1. Linkage analysis
2.1.1. Biparental mapping populations
2.1.2. Multiparent mapping populations
3. Statistical techniques used for mapping QTLs
3.1. Single marker analysis (SMA)
3.2. Simple interval mapping (SIM)
3.3. Multiple QTL mapping (MQM)
3.3.1. Composite interval mapping (CIM)
3.3.2. Multiple interval mapping (MIM)
3.3.3. Bayesian mapping
3.4. Association analysis
4. QTLs/resistance genes identified in rice
4.1. Genes identified using a biparental mapping population
4.1.1. Biotic stresses
4.1.2. Abiotic stress
4.2. Genes identified using association mapping
5. Conclusion
References
Chapter 12: Genetic improvement of rice grain quality
1. Introduction
2. Rice grain quality evaluation according to consumers preference
2.1. Cooking and eating quality
2.2. Textural and sensory quality
2.3. Nutritional quality
3. Genes/QTL for rice grain quality
3.1. Milling quality
3.2. Appearance quality (shape, size, length, and chalkiness)
3.3. Cooking quality
3.3.1. Amylose content
3.3.2. Gelatinization temperature
3.3.3. Gel consistency
4. Conclusion
References
Chapter 13: Translating genetics into genomics: From QTL identification to candidate gene discovery in rice
1. Introduction
2. Sources of genetic variation and roles of quantitative trait loci
3. Types of QTLs
3.1. Major and minor QTLs
3.2. Pleotropic QTLs
3.3. Epistatic QTLs
3.4. Expression QTLs
3.5. Metabolic QTLs
3.6. Protein and phenotypic QTLs
3.7. Meta-QTLs
4. QTL mapping
4.1. Mapping populations
4.2. Molecular markers
4.3. Mapping methods and software
5. Mining of QTL underlying candidate genes
5.1. Fine mapping
5.2. Association mapping (AM)
5.3. Meta-QTL analysis
5.4. Computational analysis
5.5. Integrated multi-omics intervention
5.6. Genome-scale knowledge networks
6. Rice improvement using functionally characterized QTLs and genes
6.1. Grain yield improvement
6.2. Grain quality improvement
6.3. Biotic and abiotic stress tolerance
7. Conclusion and future prospects
References
Chapter 14: Recent progress in molecular breeding approaches to improve drought tolerance in barley
1. Introduction
2. Bases of drought tolerance
3. Morphology and physiological mechanisms of drought stress tolerance
4. Genetic basis of drought tolerance: Four main approaches
4.1. Transcriptional regulation
4.2. Post-transcriptional regulation
4.3. QTL related to drought
4.3.1. The yield components related traits
4.3.2. Physiology-related traits
4.3.3. Morphology-related traits
4.3.4. Biochemical-related traits
4.4. Genes regulated drought tolerance in barley
5. Genome editing and functional validation of identified genes
6. Challenges and future perspectives
References
Further reading
Chapter 15: Molecular breeding for the development of drought stress tolerance in soybean
1. Molecular breeding for plant breeding
1.1. DNA markers
1.2. RFLP (restriction fragment length polymorphism)
1.3. RAPD (random amplification of polymorphic DNA)
1.4. SCARs (sequence characterized amplified regions)
1.5. SSR (simple sequence repeat)
1.6. AFLP (amplified fragment length polymorphism)
1.7. SNPs (single nucleotide polymorphism)
1.8. Application of MAS in plant breeding
1.9. MAS for qualitative character improvement
1.10. MAS for qualitative character improvement
2. Plant breeding through mutation induction
3. Improvement of drought stress tolerance in soybean
References
Chapter 16: Molecular breeding for groundnut (peanut) improvement: Present status and future prospects
1. Introduction
2. Description on different target traits for groundnut improvement
3. Genetic markers and development of genetic linkage maps
4. Trait mapping and QTL discovery
5. Molecular breeding and its achievements
6. Conclusion
References
Chapter 17: Common bean disease improvement using QTL mapping
1. Introduction
2. Genotyping for QTL mapping
3. Next-generation sequencing methods for genotyping
4. SNP arrays
5. PCR-based genotyping
6. Different mapping populations
6.1. Biparental mapping populations
6.2. Advanced inter-cross line populations
6.3. Multiple advanced generation inter-cross populations
6.4. Multiple connected biparental populations
6.5. Tools for QTL mapping analyses: Linkage map construction and QTL mapping
7. Populations used in common bean
8. Linkage map in common bean
9. Pathogen causing diseases in common bean
9.1. Anthracnose
9.2. Angular leaf spot
9.3. Rust
9.4. White mold
9.5. Root rot
9.6. Bacterial diseases
9.7. Viral diseases
9.8. Insect and nematode resistance
References
Chapter 18: Small millet improvement using molecular breeding approaches
1. Introduction
2. Origin, domestication, and taxonomy
3. Small millet improvement production constraints and breeding targets
4. Conventional breeding approaches
5. Genomic resources and genomics-assisted breeding approaches
6. Gene mapping
7. Future challenges and prospects
References
Chapter 19: An advanced breeding approach toward Sorghum improvement
1. Introduction
2. Origin and taxonomy
3. Sorghum improvement
4. Future scenario of sorghum improvement
5. Molecular diversity among cultivated and wild sorghums
6. Genetic linkage maps of sorghum
7. Marker-assisted recurrent selection
8. Genomic selection
9. MAS in sorghum
10. Conclusions
References
Index
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