Description
Springer Genetic Mapping And Marker Assisted Selection Basics Practice And Benefits 2Ed (Pb) by Boopathi N.M.
The first edition of this book, Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits, was widely appreciated as the first of its kind on this topic and has been listed as a reference work in several agricultural universities' curricula. A great deal has happened over the last five years, making it high time to incorporate recent developments in genetic mapping and report on novel strategies in marker assisted selection in crop plants as a second edition. This book addresses a range of topics, including: new marker types and their genotyping methods based on high-throughput technologies, advances in genomics and their role in new marker development, improvements in genetic mapping strategies and software updates, developments in phenomics and their applications in QTL mapping, and how to incorporate these developments and advances in marker assisted selection in crop plants. Similar to the first edition, each technique and method is explained using a step-by-step method, allowing the book to serve as a self-study guide for scholars whose work involves the genetic improvement of crop plants for any trait of interest, particularly for biotic and abiotic stress resistance.In addition, the book offers a valuable guide for undergraduate and graduate students at agricultural universities and institutes that are interested and/or involved in the genetic improvement of crop plants using modern tools. In addition, the bibliography includes a list of suggested works for pursuing further research on the topics covered. Table of Contents:- 1. Setting the Background a) Trends in Agricultural Product Demand: Functional Foods and Value Added Products b) Evolving New Crop Cultivars i. Achievements ii. Obstacles and Challenges a) Germplasm Exchange: International Laws and Governance b) Biotech Crops and Biosafety Issuesiii. Alternativesiv. Scope of genetic mapping and Marker Assisted Selectionc) Need for this Book: What can be expected? 2. Germplasm Characterization: Utilizing the Underexploited Resources a) Types of Germplasm: Natural Vs Man-made (crop specific germplasm repository, mutagenized population), Global Germplasm Resourcesb) Phenotyping for morphological and agronomic traitsi) Conventional Methods of phenotyping: Biotic and Abiotic Stress Resistance, Yield and Quality Traitsii) Recent Developments in Phenomics and Way Forwardiii) Case study in rice germplasm characterization for drought resistance: Formation of fundamental requirements iv) Traits useful for characterizationc) Allele miningd) Genetic diversity and Clusteringi) Softwareii) Principle behind the genetic diversity analysisiii) Principle of measuring goodness-of-fit of a classificatione) Genetic Diversity analysis using molecular markersf) DNA Barcoding and its utilization of germplasm exploitation g) Polymorphic Information Content and its importanceh) Diversity and Phylogenetic Tree: Importance in Mapping Population Development i) Parental selection 3. Mapping Population Developmenta) Mapping population and its importance in genetic mappingb) Selfing and Crossing techniques in crop plantsc) F2 progeniesd) F2 derived F3 (F2:3) populationse) F2 inter-matting or immortalized F2 populationsf) DH linesg) BC progeniesh) RILsi) NILs, Exotic libraries and advanced backcross populationsj) Chromosomal Segment Substitution Linesk) Backcross Inbred Linesl) Advanced Inter-cross Linesm) Recurrent Selection Backcross Populationn) Interconnected Mapping Populationso) Four-way cross population p) Multi-cross populations/Multiparent Advanced Generation Inter-cross (MAGIC) Populations q) Nested association mapping populationsr) Mapping Populations for Cross-Pollinated Speciess) Mapping Populations for autopolyploids t) Natural populationsu) Chromosome specific genetic stocks for linkage mappingv) Combining Markers and Populationsw) Characterization of Mapping Populationsx) Choice of Mapping Populationsy) Challenges in mapping population development and solutions z) Subset of Population for Bulk Segregant Analysisaa) Characterization of Mapping Populations: Size, Segregation Ratios and other properties that determines success of QTL mapping and MASbb) Selection of Mapping Populations: i) Comparisons ii) Things to be remembered 4. Genotypinga) Markers and its importanceb) Morphological markersc) Biochemical markers or Isozymesd) Molecular markerse) Genome structure and organizationf) Classification of Molecular Markers: Classical and Updated Typesg) Hybridization Based Markersi) RFLPii) Diversity Array Technology (DArT)iii) Single Feature Polymorphismiv) Other types of Microarray Based Molecular Markers h) Arbitrarily primed PCR-based markersi) RAPDii) AP-PCR and DAFiii) AFLPi) Sequence specific PCR based markersi) Microsatellite based marker techniqueii) SNP (Novel Methods to Detect, Genotyping Procedures, Utility in Genetic Mapping and MAS)iii) SFPiv) SCARv) CAPS and dCAPSvi) RAMPvii) SRAPviii) TRAPix) Start Codon-Targeted Polymorphismx) CAAT Box-Derived Polymorphismxi) Conserved DNA-Derived Polymorphismxii) Conserved Region Amplification Polymorphismxiii) Intron-Targeting Polymorphismj) Single strand conformation polymorphism k) Transposable elements (TE) based molecular markersl) Intron-Targeted Intron-Exon Splice Conjunction (IT-ISJ) Markerm) Restriction site associated DNA (RAD) markersn) RNA-based molecular markers o) Way Forward in development of new kind of molecular markers: Recent Developments in Sequence Based Molecular Markersp) Role of 'omics' in Molecular marker development (refer chapter 11)q) Selection of Marker Technology r) Marker Genotyping and Scorings) Polymorphic Information Content: Practicing with molecular markerst) Analyzing the genotype score: Chi-square testu) 2 test to analyze the segregation ratio using the program ANTMAP5. Linkage Map Constructiona) Introduction to Genome Maps: Linkage, cytogenetic and physical mapsb) Basics of linkage mapping: Mendelian rations, meiosis, crossing over and partial linkage c) Mapping function and Genetic Distance Calculation: Methods and Proceduresd) Mapping of genetic markers: genetic consideration, general procedure and validatione) Testing of linkage: LOD scores, Threshold, Comparison and Confirmationf) Fine Tuning the Linkage: Grouping, ordering and spacingg) Methods to Detect and Avoid Sources of Errorh) Chromosomal assignmenti) Allopolyploidy and autopolyploidy j) Bridging linkage maps to develop unified linkage mapsk) High-Resolution Mappingl) Mapping of Major Genes: Strategies, Methods and Proceduresm) Selective Genotyping and Mapping: Basics and Procedure n) Merging Linkage Maps to Cytogenetic Maps and Physical Maps: Genetic Considerationso) Software for Linkage Mapping: i) List of Linkage Mapping Software and Basic Understanding ii) Considerations for Selection of Best Software6. Phenotypinga) Phenomicsi. Advances in Phenomicsii. Applications in QTL mapping b) Phenotyping vs. QTL mappingc) Need for precise phenotypingd) Phenotyping for biotic stressi. Explaining the concept with a Case studye) Phenotyping for abiotic stressi. Explaining the concept with a Case studyf) Heritability of phenotypesg) Statistical analysis of phenotypic datai. Simple Statistics ii. Heritability Estimation iii. Correlation Analysis7. QTL Identificationa) QTL: a prelude b) Single marker analysis: Principle, Methods and Procedurec) Interval mapping: Principle, Methods and Procedured) Multiple QTLs: Principle, Methods and Proceduree) Composite interval mapping: Principle, Methods and Proceduref) QTL mapping software: i) List of QTL Mapping Software and Basic Understanding ii) Considerations for Selection of Best Softwareg) Multiple trait mappingh) Testing for linked vs. pleiotropic QTLsi) Multiple interval mapping or multiple QTL mappingj) Statistical significancek) Permutation testingl) Bootstrapping m) Permutation vs. bootstrapping and other methods n) QTL x QTL interaction: impact of epistasiso) QTL x Environment interactionp) Congruence of QTLs: across the environments and across the genetic backgrounds is the key in MASq) Meta-QTL analysisr) Concluding remarks on QTL methodss) Alternatives in classical QTL mapping: Understanding and Practicing Different Strategies t) Bulked segregant analysis and selective genotyping: Basics, genetic considerations and Procedures u) Genomics assisted breeding: Basics, genetic considerations and Procedures v) Array mapping: Basics, genetic considerations and Procedures w) Association mapping: Basics, genetic considerations and Procedures x) Nested association mapping: Basics, genetic considerations and Procedures y) EcoTILLING: Basics, genetic considerations and Procedures z) Challenges and Troubleshooting in QTL mapping aa) Way forward to incorporate into regular crop breeding program8. Fine Mappinga) Need for fine mapping or high resolution mappingb) Types of markers suitable for fine mappingi. Marker Type Conversionc) Physical mapping and its role in fine mappingd) Comparative mappinge) Genetical genomics or eQTL mappingf) Map based cloningi. Explaining with case studies g) Validation of QTLh) Testing the markers in related germplasm accessions9. Marker Assisted Selectionsa) Prelude b) Why should we use MAS?c) What prevents the use of MAS?d) Prerequisites for an efficient marker assisted programe) Procedure for generalized MAS program for selection from breeding lines / populationsf) Marker assisted back cross breeding: Principles and Proceduresg) Gene pyramiding or stacking: Principles and Proceduresh) Accelerated methods of gene pyramiding: Principles and Proceduresi) Marker assisted recurrent selection: Principles and Proceduresj) AB-QTL: Principles and Proceduresk) Mapping-as-you-go: Principles and Procedures l) Application of MAS in germplasm storage, evaluation and usem) Resources for MAS on the web10. Success Stories in MASa) MAS in Major Crop: Tomatob) MAS in Major Crop: Maizec) MAS in Major Crop: Wheatd) MAS in Major Crop: Ricee) MAS in Major Crop: Cottonf) MAS in Major Crop: Soybeang) Varieties released through MASh) Hybrids released through MASi) MAS in multinational companiesj) Contrasting storiesk) Conclusions and future prospects11. Towards genetically improved crop plants: Roles of 'Omics and MAS a) Molecular breeding platformsi. Comparisons of Techniques in molecular, biochemical and physiological studies and its integration into MASb) Prelude on Molecular techniquesc) Expression profilingd) cDNA library constructione) Differential display and representational difference analysisf) Subtractive hybridization g) Microarrayh) Nucleic acid sequencing i) Serial analysis of gene expression (SAGE)j) cDNA-AFLPk) RFLP coupled domain directed differential display (RC4D)l) Gene tagging by insertional mutagenesism) Post transcriptional gene silencingn) microRNAso) Biochemical techniquesp) Proteomicsq) Genomics assisted breedingr) Functional markerss) Comparative genomicst) Identification of novel molecular networks and construction of new metabolic pathwayu) Bioinformatics and MAS12. Forthcoming Perspectives in MASa) MAS in orphan cropsb) MAS in Horticultural Crops: i. Vegetables, ii. Fruit Crops, iii. Medicinal and Aromatic Crops iv. Landscaping Plantsc) MAS in developing countriesd) Perspectives of MAS in Commercial Breeding Program e) Community efforts and their implications in MASf) Field and laboratory infrastructure improvement g) Genetic Mapping and MAS: Lessons learnt and concluding remarksshow more