全新正版连锁分析与基因定位:英文9787030757616科学出版社

Contents

Preface III

CHAPTER 1 PopulationsinGeneticStudies 1

1.1 CommonlyUsedPopulationsinGeneticStudies 2

1.1.1 Bi-ParentalPopulations 2

1.1.2 Multi-ParentalPopulations 5

1.1.3 Considerations in Developing Genetic Populations 9

1.2 PreliminaryAnalysisofGenotypicData 12

1.2.1 CollectionandCodingofGenotypicData 12

1.2.2 Gene Frequency and Genotypic Frequency 17

1.. FitnessTestonGenotypicFrequencies 18

1.3 GeneticEffectandGeneticVariance 20

1.3.1 Calculation of Population Mean and Phenotypic Variance 20

1.3.2 One-Locus Additive and Dominance Model

1.3.3 Population Mean and Genetic Variance at One Locus 24

1.4 ANOVAonSingleEnvironmentTrials 27

1.4.1 Linear Decoition on Phenotypic Observation 27

1.4.2 Decoition of Sum of Squares of Phenotypic Deviations 28

1.4.3 Single Environmental ANOVA on Rice Grain Length 31

1.5 ANOVAonMulti-EnvironmentTrials 32

1.5.1 Linear Decoition on Phenotypic Observation 32

1.5.2 Decoition of Sum of Squares of Phenotypic Deviations 33

1.5.3 Multi-Environmental ANOVA on Rice Grain Length 38

1.6 Estimation of Genotypic Values and the Broad-Sense Heritability 39

1.6.1 Genotypic Values and Broad-Sense Heritability fromSingleEnvironmentalTrials 39

1.6.2 Genotypic Values and Broad-Sense Heritability fromMulti-EnvironmentalTrials 41

1.6.3 Estimation of Genotypic Values Under Heterogeneous Error Variances 42 Exercises 45

CHAPTER 2 Estimation of the Two-Point Recombination Frequencies 51

2.1 GenerationTransitionMatrix 51

2.1.1 Usefulness of the Transition Matrix in Linkage Analysis 51

2.1.2 Transition Matrix of One Generation of Backcrossing 53

2.1.3 Transition Matrix of One Generation of Selfing 55

2.1.4 TransitionMatrixofDoubledHaploid 58

2.1.5 TransitionMatrixofRepeatedSelfing 59

2.1.6 Expression of the Two-Locus Genotypic Frequencies inMatrixFormat 61

2.2 Theoretical Genotypic Frequencies at Two Loci 62

2.2.1 Theoretical Frequencies of 10 Genotypes at Two Loci 62

2.2.2 Theoretical Frequencies of 4 Homozygotes in Permanent Populations 65

2.. Genotypic Frequencies of Two Co-Dominant Loci inTemporaryPopulations 65

2.2.4 Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations 69

2.2.5 Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations 69

2.2.6 Genotypic Frequencies of Two Dominant Loci in Temporary Populations 74

2.2.7 Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations 74

2.2.8 Genotypic Frequencies of Two Recessive Loci in Temporary Populations 77

. Estimation of Two-Point Recombination Frequency 77

..1 Maximum Likelihood Estimation of Recombination FrequencyinDHPopulations 77

..2 General Procedure on the Maximum Likelihood Estimation ofRecombinationFrequency 81

.. Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 population 86

..4 InitialValuesinNewtonAlgorithm 87

..5 EM Algorithm in Estimating Recombination Frequency in F2 Populations 90

.. Effects on the Estimation of Recombination Frequency from SegregationDistortion 92

Exercises 95

CHAPTER 3 Three-Point Analysis and Linkage Map Construction 101

3.1 Three-Point Analysis and Mapping Function 102

3.1.1 Genetic Interference and Coefficient of Interference 102

3.1.2 Mapping Function 105

3.2 ConstructionofGeneticLinkageMaps 107

3.2.1 MarkerGroupingAlgorithm 107

3.2.2 MarkerOrderingAlgorithm 111

3.. Use of the -Otial Algorithm in Linkage Map Construction 113

3.2.4 RipplingoftheOrderedMarkers 117

3.2.5 IntegrationofMultipleMaps 118

3.3 Comparison of the Recombination Frequency Estimation in Different Populations 121

3.3.1 LOD Score in Testing the Linkage Relationship in Different Populations 121

3.3.2 Accuracy of the Estimated Recombination Frequency 1

3.3.3 Least Population Size to Declare the Significant Linkage RelationshipandCloseLinkage 124

3.4 Linkage Analysis in Random Mating Populations 127

3.4.1 Linkage Dis-Equilibrium in Random Mating Populations 127

3.4.2 Generation Transition Matrix from Diploid Genotypes toHaploidGametes 130

3.4.3 Gametic and Genotypic Frequencies in Populations After SeveralGenerationsofRandomMating 132 Exercises 134

CHAPTER 4 Single Marker Analysis and Simple Interval Mapping 139

4.1 SingleMarkerAnalysis 140

4.1.1 Phenotypic Means of Different Genotypes at One Marker Locus 140

4.1.2 Single Marker Analysis by t-Test in Populations with Two Genotypes 143

4.1.3 Single Marker Analysis by t-Test in Populations with Three Genotypes 146

4.1.4 ANOVA in Single Marker Analysis in Populations with Three Genotypes 150

4.1.5 Likelihood Ratio Test in Single Marker Analysis 151

4.1.6 ProblemswithSingleMarkerAnalysis 153

4.2 SimpleIntervalMapping 154

4.2.1 Frequencies of the TL Genotypes in a Marker Interval 154

4.2.2 Maximum Likelihood Estimation of Phenotypic Means ofTLGenotypes 161

4.. TestingfortheExistenceofTL 166

4.2.4 Estimation of Genetic Effects of TL and Its Contribution toPhenotypicVariance 167

4.2.5 Applications of Simple Interval Mapping in DH and F2 Populations 168

4.2.6 Phenomenon of ‘Ghost’ TL in Simple Interval Mapping 171

4.2.7 Other Problems with Simple Interval Mapping 172

4.3 ThresholdValuesofLODScoreinTLMapping 174

4.3.1 Significance Level and Critical Value of One Test Statistic 174

4.3.2 Distribution of the LRT Statistic at Single Scanning Positions intheAbsenceofAnyTL 176

4.3.3 Factors Affecting the Distribution of the Genome-Wide LargestLODScore 177

4.3.4 Number of Effective Tests and the Empirical LOD Score ThresholdsinTLMapping 180

4.3.5 Permutation Test and the Empirical LOD Score Thresholds inTLMapping 184 Exercises 189

CHAPTER 5 InclusiveCoiteIntervalMapping 195

5.1 Importance of the Control on Background Genetic Variation in TL Mapping 196

5.2 Inclusive Coite Interval Mapping in DH Populations 199

5.2.1 AdditiveGeneticModelofOneSingleTL 199

5.2.2 Additive Genetic Model for Multiple TLs 201

5.. One-Dimensional Scanning and Hypothesis Testing forAdditiveTLs 202

5.2.4 Application of ICIM in a DH Mapping Population in Barley 204

5.3 Inclusive Coite Interval Mapping in F2 Populations 208

5.3.1 Additive and Dominant Model of One Single TL 208

5.3.2 Additive and Dominant Model for Multiple TLs 212

5.3.3 One-Dimensional Scanning and Hypothesis Testing inAdditiveandDominantTLMapping 213

5.3.4 Application of ICIM in an F2 Mapping Population 214

5.4 Type II Error in Hypothesis Testing and Statistical Power in TL Detection 216

5.4.1 Type II Error and Statistical Power in Hypothesis Testing 216

5.4.2 Probability of Two Types of Error and the Appropriate SampleSize 220

5.4.3 Distribution and Effect Models of TLs Used in Power AnalysisbySimulations 222

5.4.4 Calculation of the Detection Power and False Discovery Rate inTLMapping 224

5.5 ComparisonofIMandICIMbySimulation 0

5.5.1 TLDetectionPowerandFDRfromIM 0

5.5.2 TLDetectionPowerandFDRfromICIM 2

5.5.3 Detection Powers Counted by Marker Intervals 4

5.5.4 Suitable Population Size Required in TL Mapping 5

5.6 Avoiding the Overfitting Problem in the First Step of Model SelectioninICIM Exercises 240

CHAPTER 6 TL Mapping for Epistasis and Genotype-by-Environment Interaction 245

6.1 EpistaticTLMappinginDHPopulations 246

6.1.1 Linear Regression in Epistatic TL Mapping and the StatisticalProperties 246

6.1.2 Two-Dimensional Scanning on Di-Genic Epistatic TLs 248

6.1.3 Genetic Variance on Epistatic TLs with Linkage 253

6.1.4 Simulation Study on Epistatic TL Mapping in DH Populations 254

6.2 EpistaticTLMappinginF2Populations 257

6.2.1 The Di-Genic Epistasis Model in F2 Populations 257

6.2.2 Epistatic TL Mapping Procedure in F2 Population 258

6.. Detection Power of Epistatic TLs in F2 Populations 265

6.3 Genetic Analysis and Detection Power of the Most Common Di-GenicInteractions 268

6.3.1 Genetic Effects in Di-Genic Interactions 268

6.3.2 Decoition of Genetic Variance at the Presence ofDi-GenicEpistasis 270

6.3.3 Power Simulation of Epistatic TL Mapping 276

6.3.4 IssuesinEpistaticTLMapping 281

6.4 Mapping of the TL by Environment Interactions 282

6.4.1 Mapping of the Additive TL by Environment Interactions 282

6.4.2 Mapping of the Epistatic TL and Environment Interactions 285

6.4.3 TL and Environment Interactions in One Actual RIL PopulationinMaize 287 Exercises 291

CHAPTER 7 Genetic Analysis in Hybrid F1 of Two Heterozygous Parents andDouble-CrossF1ofFourHomozygousParents 295

7.1 Linage Analysis in the Hybrid F1 Derive fo Two Heterozygous Parents 296

7.1.1 CategoriesofPolymorphismMarkers 296

7.1.2 Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci 298

7.1.3 Estimation of the Recombination Frequency Between Two Fully-InformativeMa

本书建立在作者十多年科研和教学的基础之上，全书可分为三部分。章为部，介绍遗传研究群体，主要内容包括常见群体类型、基因型数据的初步整理和分析、基因效应和遗传方差的定义和计算、单环境和多环境表型观测值的方差分析、以及基因型值和遗传力的估计等内容。第~章为第二部分，介绍双亲群体连锁分析和遗传图谱构建，主要内容包括世代转移矩阵、两个座位上基因型的理论频率、两个基因座位间重组率的估算、作图函数和遗传图谱构建算法等内容。第4~10章为第三部分，介绍数量状基因的作图原理和方法，主要内容包括单标记分析、简单区间作图、完备区间作图方法、上位型互作、与环境互作的TL作图，以及有选择群体、自然群体、无系杂群体和多亲本群体的基因定位等内容。