Plant omics : trends and applications / Khalid Rehman Hakeem, Hüseyin Tombuloğlu, Güzin Tombuloğlu, editors.
To comprehend the organizational principle of cellular functions at diff erent levels, an integrative approach with large-scale experiments, the so-called?omics? data including genomics, transcriptomics, proteomics, and metabolomics, is needed. Omics aims at the collective characterization and quant...
Saved in:
| Online Access: |
Full Text (via Springer) |
|---|---|
| Other Authors: | , , |
| Format: | eBook |
| Language: | English |
| Published: |
Switzerland :
Springer,
2016.
|
| Subjects: |
Table of Contents:
- Dedication; Foreword; Preface; Contents; About the Editors; Genome Analysis of€Plants; 1 Introduction; 2 The Genetic Structure of€Plant Genomes; 2.1 Genetic Maps; 2.2 Physical Maps; 3 Plant Genome Annotation; 3.1 Plant Genome Databases; 3.2 Repeat Masking; 3.3 Structural Annotation; 3.3.1 Ab Initio Methods; 3.3.2 Homology-Based Methods; 3.3.3 Integrated Methods; 3.4 Functional Annotation; 3.4.1 Domain Search; 3.4.2 Gene Ontology; 4 Molecular Phylogenetics; 5 Comparative Plant Genomics; 5.1 Orthologs and€Paralogs; 5.2 Synteny, Duplication, and€Polyploidy.
- 5.3 Web Resources for€Comparative Genomics6 Conclusion; References; Genomics Resources for€Plants; 1 Introduction; 2 1000 Plants (oneKP or 1KP); 3 Amborella Genome Database; 4 BAR; 5 Cacao Genome Database (CGD); 6 CerealsDB; 7 Gramene; 8 Kazusa Tomato Genomics Database (KaTomicsDB); 9 Parasitic Plant Genome Project (PPGP); 10 Plant Genome DataBase Japan (PGDBj); 11 Plant Genome Duplication Database (PGDD); 12 Plant Genome and€Systems Biology (PGSB); 13 Phytozome; 14 Plant Repeat Databases; 15 PLAZA; 16 Plant Expression Database (PLEXdb); References.
- QTL Analysis in€Plants: Ancient and€Modern Perspectives1 Introduction; 1.1 Quantitative Trait Loci; 1.2 Essentiality of€QTL Analysis; 1.3 Principle of€QTL Analysis; 2 Methodology Involved; 2.1 Mapping Population; 2.2 Genotyping; 2.3 Phenotyping; 2.4 Software Used; 2.4.1 QTL Cartographer; 2.4.2 MQTL; 2.4.3 MapQTL; 2.4.4 Joinmap; 2.4.5 Map Manager; 2.4.6 QGene; 2.4.7 SAS; 2.5 Interpreting Results; 2.5.1 Isolation of€Linked Markers; 2.5.2 Mapping Function; 2.5.3 Single-Marker Analysis; 2.5.4 Interval Mapping; 3 Modern Perspectives in€QTL Analysis; 3.1 Genotyping to€Genomics.
- 3.2 Phenotyping to€Phenomics3.3 Multiparent Advanced Generation Inter-Cross (MAGIC) Populations; 3.4 Next-Generation Sequencing (NGS); 4 Practical Potential of€QTL Analysis; 4.1 Crops with€Improved Breeding Strategies; 4.2 Revealing the€Genetic Bases of€Abiotic Stress Tolerance; 4.3 Exposing Genetic Dissection of€Biotic Stress Resistance; 5 Conclusions and€Future Perspective; References; Transposon Activity in€Plant Genomes; 1 Introduction; 2 Structure of€Transposons; 3 Types and€Classification of€Transposons; 3.1 Class I€Transposons (Retrotransposons); 3.1.1 Order 1: LTR Retrotransposons.
- 3.1.2 Order 2: DIRS3.1.3 Order 3: PENELOPE (PLE); 3.1.4 Order 4: LINE; 3.1.5 Order 5: SINE; 3.2 Class II Transposons (DNA Transposons); 3.2.1 Subclass I€Order I: TIR; 3.2.2 Subclass I€Order II: Crypton; 3.2.3 Subclass II Order I: Helitron; 3.2.4 Subclass II Order II: Maverick; 3.3 Transposons in€Different Plant Species; 4 Transposon Markers; 4.1 Inter-Retrotransposon Amplified Polymorphism (IRAP); 4.2 Retrotransposon-Microsatellite-Amplified Polymorphism (REMAP); 4.3 Retrotransposon-Based Insertional Polymorphism (RBIP); 4.4 Sequence-Specific Amplified Polymorphism (S-SAP)