Statistical Genomics Linkage, Mapping, and QTL Analysis

About this book

Provides comprehensive up-to-date coverage on statistical methods and theory used in genomic analyses.

Contents

IntroductionForwardIntroducing GenomicsStatistical GenomicsRelated BooksBiology in GenomicsIntroductionMendelian Genetics and CytogeneticsPopulation GeneticsQuantitative GeneticsMolecular GeneticsExercisesIntroduction to GenomicsGenomeGenomicsGenetic MarkersExercisesStatistics in GenomicsIntroductionDistribution LikelihoodHypothesis TestEstimationSample Size DeterminationSummaryExercisesSingle-Locus ModelsIntroductionExpected Segregation RatioMarker ScreeningNatural PopulationExercisesTwo-Locus Models I: Controlled CrossIntroductionLinkage DetectionRecombination Frequency EstimationStatistical PropertiesSample Size ConsiderationDominant Markers in F2 ProgenyViolation of AssumptionsSummaryExercisesTwo-Locus Model II: Natural PopulationIntroductionLinkage Phase ProblemMixture of Self and Random MatingExercisesTwo-Locus Model III: Using DisequilibriumIntroductionLinkage DisequilibriumTransmission Disequilibrium TestOther Disequilibrium Based AnalysisEstimation of Recombination FrequencyExercisesLinkage Grouping and Locus OrderingIntroductionLinkage GroupingThree-Locus OrderingMultiple-Locus OrderingProbability of Estimated Locus OrdersExerciseMulti-Locus ModelIntroductionThree-Locus ModelMap FunctionMulti-Locus Map DistanceMarker Coverage and Map DensityExercisesLinkage Map MergingIntroductionFactors Related to Linkage Map MergingHypothesis on Gene OrdersLinkage Map PoolingExercisesQTL Mapping I: IntroductionHistoryQuantitative Genetics ModelsExample DataExerciseQTL Mapping II: Single-Marker AnalysisRationaleSingle-Marker Analysis in Backcross ProgenySingle Marker Analysis Using F2 ProgenySummaryExercisesQTL Mapping III: Interval MappingIntroductionInterval Mapping Using Backcross ProgenyInterval Mapping Using F2 ProgenyComposite Interval MappingSummaryExercisesQTL Mapping IV: Natural PopulationIntroductionOpen-Pollinated PopulationsSib-Pair MethodExercisesQTL Mapping V: PowerIntroductionSingle QTL Detection PowerMultiple QTLExercisesQTL Mapping VI: Future ConsiderationsProblems with QTL MappingQTL ResolutionMapping StrategiesWhat are QTLFuture QTL MappingExercisesComputer ToolsComputer Tools for Genomic Data AnalysisFuture ConsiderationsPGRI (Plant Genome Research InitiativeResampling and Simulation in GenomicsIntroductionResamplingComputer SimulationMapping Population SimulationExercisesBibliographyAuthor IndexSubject Index

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