Genetic Mapping and Marker Assisted Selection

1.Germplasm Characterization: Utilizing the Underexploited Resources.- i)Phenotyping for morphological and agronomic traits.- i) Case study in rice germplasm characterization for drought resistance: Formation of fundamental requirements.- ii) Traits useful for characterization.- b)Allele mining.- c) Genetic diversity and Clustering.- i) Software.- ii) Principle behind the genetic diversity analysis.- iii) Principle of measuring goodness-of-fit of a classification.- d) Genetic Diversity analysis using molecular markers.- e) Parental selection.- 2. Mapping Population Development.- a)Mapping population and its importance in genetic mapping.- b) Selfing and Crossing techniques in crop plants.- c) F2 progenies.- d) F2 derived F3 (F2:3) populations.- e) F2 inter-mattingor immortalized F2 populations.- f)DH lines.- g) BC progenies.- h) RILs.- i) NILs, Exotic libraries and advanced backcross populations.- j) Four-way cross population.- k) Multi-cross populations.- l) Nested association mapping populations.- m) Natural populations.- n) Chromosome specific genetic stocks for linkage mapping.- o) Combining Markers and Populations.- p) Characterization of Mapping Populations.- q) Choice of Mapping Populations.- r) Challenges in mapping population development and solutions to these challenges.- s) Bulk Segregant Analysis.- 3. Genotyping.- a) Markers and its importance.- b)Morphological markers.- c) Biochemical markers or Isozymes.- d) Genome structure and organization.- e) Molecular markers.- f) RFLP.- g) Arbitrarily primed PCR-based markers.- i) RAPD.- ii) AP-PCR and DAF.- iii) AFLP.- h)Sequence specific PCR based markers.- i) Microsatellite based marker technique.- ii) SNP.- iii) SFP.- iv) SCAR.- v) CAPS and dCAPS.- vi) RAMP.- vii) SRAP.- viii) TRAP.- i) Single strand conformation polymorphism.- j)Transposable elements (TE) based molecular markers.- k) Diversity Array Technology (DArT).- l) Intron-Targeted Intron-Exon Splice Conjunction (IT-ISJ) Marker.- m) Restriction site associated DNA (RAD) markers.- n) RNA-based molecular markers.- o) Role of genomics.- p) Selection of Marker Technology.- q) Marker Genotyping and Scoring.- r) Analyzing the genotype score: Chi-square test.- s) ?2 test to analyze the segregation ratio using the program ANTMAP.- 4. Linkage Map Construction.- a)Basics of linkage mapping: Mendelian rations, meiosis, crossing over and partial linkage.- b) Mapping function.- c) Mapping of genetic markers: genetic consideration.- d) Testing of linkage: LOD scores.- e) Grouping, ordering and spacing.- f) Sources of error.- g) Chromosomal assignment.- h)Allopolyploidy and autopolyploidy.- i) Bridging linkage maps to develop unified linkage maps.-5. Phenotyping.- a) Phenotyping vs. QTL mapping.- b) Need for precise phenotyping.- c) Phenotyping for biotic stress.- d)Phenotyping for abiotic stress.- e) Heritability of phenotypes.- f)Statistical analysis of phenotypic data: simple statistics, heritability estimation and correlation.- 6. QTL Identification.- a) QTL: a prelude.- b)Single marker analysis.- c) Interval mapping.- d) Multiple QTL and methods to detect multiple QTL.- e) Composite interval mapping.- f) Multiple trait mapping.- g) Testing for linked vs. pleiotropic QTLs.- h) Multiple interval mapping or multiple QTL mapping.- i) Statistical significance.- j)Permutation testing.- k) Bootstrapping.- l) Permutation vs. bootstrapping and other methods.- m) QTL x QTL interaction: impact of epistasis.- n)QTL x Environment interaction.- o) Congruence of QTLs: across the environments and across the genetic backgrounds is the key in MAS.- p)Meta-QTL analysis.- q) Concluding remarks on QTL methods.- r)Alternatives in classical QTL mapping.- s) Bulked segregant analysis and selective genotyping.- t) Genomics assisted breeding.- u) Array mapping.- v) Association mapping.- w) Nested association mapping.- x) EcoTILLING.- y) Challenges in QTL mapping.- 7. Fine Mapping.- a) Need for fine mapping or high resolution mapping.- b) Types of markers suitable for fine mapping.- c) Physical mapping and its role in fine mapping.- d) Comparative mapping.- e) Genetical genomics or eQTL mapping.- f) Map based cloning.- g)Validation of QTL.- h) Testing the markers in related germplasm accessions.- 8. Marker Assisted Selections.- a) Advantages of MAS.- b)Limitations in MAS.- c) Prerequisites for an efficient marker assisted program.- d) Procedure for generalized MAS program for selection from breeding lines / populations.- e) Marker assisted back cross breeding.- f)Gene pyramiding or stacking.- g) Accelerated methods of gene pyramiding.- h) Marker assisted recurrent selection.- i) AB-QTL.- j)Mapping-as-you-go.- k) Application of markers in germplasm storage, evaluation and use.- l) Resources for MAS on the web.- 9. Success Stories in MAS.- a) Tomato.- b) Maize.- c) Wheat.- d) Rice.- e) Barley.- f) Soybean.- g) Varieties released through MAS.- h) Hybrids released through MAS.- i)MAS in multinational companies.- j) Contrasting stories.- k)Conclusions and future prospects.- 10. Advances in MAS toward genetically improved crop plants.- a) Molecular breeding platforms: Techniques in molecular, biochemical and physiological studies and its integration into MAS.- b)Molecular techniques.- c) Expression profiling.- d) cDNA library construction.- e) Differential display and representational difference analysis.- f) Subtractive hybridization.- g) Microarray.- h) Nucleic acid sequencing.- i) Serial analysis of gene expression (SAGE).- j)cDNA-AFLP.- k) RFLP coupled domain directed differential display (RC4D).- l)Gene tagging by insertional mutagenesis.- m) Post transcriptional gene silencing.- n) microRNAs.- o) Biochemical techniques.- p) Why proteomics?.- q) Type of proteomics.- r) Protein analysis.- s) One - and two - dimensional gel electrophoresis .- t) Alternatives to electrophoresis in proteomics.- u)Acquisition of protein structure information.- v) Edman sequencing.- w)Mass spectrometry.- x) Types of mass spectrometers.- y) Peptide fragmentation.- z) De novo peptide sequence information.- aa)Uninterpreted MS/MS data searching.- bb) Proteomics approach to protein phosphorylation.- cc) Phosphoprotein enrichment.- dd)Phosphorylation site determination by Edman sequencing.- ee)Phosphorylation site determination by mass spectrometry.- ff) Metabolite profiling technologies.- gg) Physiological techniques.- hh) Near infrared spectroscopy.- ii) Canopy spectral reflectance (CSR) and infrared thermography (IRT).- jj) Estimation of compatible solutes.- kk) Genomics assisted breeding.- ll) Functional markers.- mm) Comparative genomics.- nn) Identification of novel molecular networks and construction of new metabolic pathway.- oo) Bioinformatics for MAS.- 11. Recent advances in MAS in major crops.- a) Rice.- b) Cotton.- c) Mungbean.- d) Tomato.- e)Hot-pepper.- 12. Future perspectives in MAS.- a) MAS in orphan crops.- b)MAS in developing countries.- c) Community efforts and their implications in MAS.- d) Field and laboratory infrastructure improvement.- e) Lessons learnt and concluding remarks.