Preface CHAPTER 1 PopulationsinGeneticStudies 1.1 CommonlyUsedPopulationsinGeneticStudies 1.1.1 Bi-ParentalPopulations 1.1.2 Multi-ParentalPopulations 1.1.3 Considerations in Developing Genetic Populations 1.2 PreliminaryAnalysisofGenotypicData 1.2.1 CollectionandCodingofGenotypicData 1.2.2 Gene Frequency and Genotypic Frequency 1.2.3 FitnessTestonGenotypicFrequencies 1.3 GeneticEffectandGeneticVariance 1.3.1 Calculation of Population Mean and Phenotypic Variance 1.3.2 One-Locus Additive and Dominance Model 1.3.3 Population Mean and Genetic Variance at One Locus 1.4 ANOVAonSingleEnvironmentTrials 1.4.1 Linear Decomposition on Phenotypic Observation 1.4.2 Decomposition of Sum of Squares of Phenotypic Deviations 1.4.3 Single Environmental ANOVA on Rice Grain Length 1.5 ANOVAonMulti-EnvironmentTrials 1.5.1 Linear Decomposition on Phenotypic Observation 1.5.2 Decomposition of Sum of Squares of Phenotypic Deviations 1.5.3 Multi-Environmental ANOVA on Rice Grain Length 1.6 Estimation of Genotypic Values and the Broad-Sense Heritability 1.6.1 Genotypic Values and Broad-Sense Heritability fromSingleEnvironmentalTrials 1.6.2 Genotypic Values and Broad-Sense Heritability fromMulti-EnvironmentalTrials 1.6.3 Estimation of Genotypic Values Under Heterogeneous Error Variances 42 Exercises CHAPTER 2 Estimation of the Two-Point Recombination Frequencies 2.1 GenerationTransitionMatrix 2.1.1 Usefulness of the Transition Matrix in Linkage Analysis 2.1.2 Transition Matrix of One Generation of Backcrossing 2.1.3 Transition Matrix of One Generation of Selfing 2.1.4 TransitionMatrixofDoubledHaploid 2.1.5 TransitionMatrixofRepeatedSelfing 2.1.6 Expression of the Two-Locus Genotypic Frequencies inMatrixFormat 2.2 Theoretical Genotypic Frequencies at Two Loci 2.2.1 Theoretical Frequencies of 10 Genotypes at Two Loci 2.2.2 Theoretical Frequencies of 4 Homozygotes in Permanent Populations 2.2.3 Genotypic Frequencies of Two Co-Dominant Loci inTemporaryPopulations 2.2.4 Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations 2.2.5 Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations 2.2.6 Genotypic Frequencies of Two Dominant Loci in Temporary Populations 2.2.7 Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations 2.2.8 Genotypic Frequencies of Two Recessive Loci in Temporary Populations 2.3 Estimation of Two-Point Recombination Frequency 2.3.1 Maximum Likelihood Estimation of Recombination FrequencyinDHPopulations 2.3.2 General Procedure on the Maximum Likelihood Estimation ofRecombinationFrequency 2.3.3 Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 population 2.3.4 InitialValuesinNewtonAlgorithm 2.3.5 EM Algorithm in Estimating Recombination Frequency in F2 Populations 2.3.6 Effects on the Estimation of Recombination Frequency from SegregationDistortion Exercises CHAPTER 3 Three-Point Analysis and Linkage Map Construction 3.1 Three-Point Analysis and Mapping Function 3.1.1 Genetic Interference and Coefficient of Interference 3.1.2 Mapping Function 3.2 ConstructionofGeneticLinkageMaps 3.2.1 MarkerGroupingAlgorithm 3.2.2 MarkerOrderingAlgorithm 3.2.3 Use of the k-Optimal Algorithm in Linkage Map Construction 3.2.4 RipplingoftheOrderedMarkers 3.2.5 IntegrationofMultipleMaps 3.3 Comparison of the Recombination Frequency Estimation in Different Populations 3.3.1 LOD Score in Testing the Linkage Relationship in Different Populations 3.3.2 Accuracy of the Estimated Recombination Frequency 3.3.3 Least Population Size to Declare the Significant Linkage RelationshipandCloseLinkage 3.4 Linkage Analysis in Random Mating Populations 3.4.1 Linkage Dis-Equilibrium in Random Mating Populations 3.4.2 Generation Transition Matrix from Diploid Genotypes toHaploidGametes 3.4.3 Gametic and Genotypic Frequencies in Populations After SeveralGenerationsofRandomMating 132 Exercises CHAPTER 4 Single Marker Analysis and Simple Interval Mapping 4.1 SingleMarkerAnalysis 4.1.1 Phenotypic Means of Different Genotypes at One Marker Locus 4.1.2 Single Marker Analysis by t-Test in Populations with Two Genotypes 4.1.3 Single Marker Analysis by t-Test in Populations with Three Genotypes 4.1.4 ANOVA in Single Marker Analysis in Populations with Three Genotypes 4.1.5 Likelihood Ratio Test in Single Marker Analysis 4.1.6 ProblemswithSingleMarkerAnalysis 4.2 SimpleIntervalMapping 4.2.1 Frequencies of the QTL Genotypes in a Marker Interval 4.2.2 Maximum Likelihood Estimation of Phenotypic Means ofQTLGenotypes 4.2.3 TestingfortheExistenceofQTL 4.2.4 Estimation ���� CHAPTER 5 Inclusive Composite Interval Mapping CHAPTER 6 QTL Mapping for Epistasis and Genotype-by-Environment Interaction CHAPTER 7 Genetic Analysis in Hybrid F1 of Two Heterozygous Parentsana Domble-Cross F1 of Four Homozygous Parents CHAPTER 8 Genetic Analysis in Multi-Parental Pure-Line Progeny Populations. CHAPTER 9 QTL Mapping in Other Genetic Populations CHAPTER 10 More on the Frequently Asked Questions in QTL Mapping References Index Appendix A��Journal Articles Making Up This Book Appendix B��Dissertations of Post-Graduates Making Up This Book Appendix C��Integrated Software Packages Making Up This Book