Genetic Mapping and Marker Assisted Selection

1.Germplasm Utilizing the Underexploited Resources.- i)Phenotyping for morphological and agronomic traits.- i) Case study in rice germplasm characterization for drought 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 ( 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 Chi-square test.- s) Χ2 test to analyze the segregation ratio using the program ANTMAP.- 4. Linkage Map Construction.- a)Basics of linkage Mendelian rations, meiosis, crossing over and partial linkage.- b) Mapping function.- c) Mapping of genetic genetic consideration.- d) Testing of 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 simple statistics, heritability estimation and correlation.- 6. QTL Identification.- a) 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 impact of epistasis.- n)QTL x Environment interaction.- o) Congruence of 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