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laboutique.edpsciences.fr-R001903 03 01 01 R001903 00 ED E107 00 01 01 Linkage Analysis and Gene Mapping 01 eng 08 532 03 22 15106915 17 01 P15 EDP Sciences & Science Press 01 01 P15 EDP Sciences & Science Press 11 00 20230707 02 01 002280 03 9782759830435 15 9782759830435 03 01 D1 EDP Sciences 45 03 laboutique.edpsciences.fr-002280 03 01 01 002280 03 9782759830435 15 9782759830435 10 EA E107 10 00 01 R001903 ED E107 1 10 01 02 Current Natural Sciences 01 01 Linkage Analysis and Gene Mapping 1 A01 01 A2151 Jiankang WANG WANG, Jiankang Jiankang WANG 2 A01 01 A2150 Huihui LI LI, Huihui Huihui LI 3 A01 01 A2149 Luyan ZHANG ZHANG, Luyan Luyan ZHANG 01 eng 08 530 03 01 24 Izibook:Subject Sciences de la vie 24 Izibook:SubjectAndCategoryAndTags |Sciences de la vie| 20 genetic;linkage analysis;biochemical;self-pollinated;cross-pollinated 10 2011 SCI029000 01 570 06 05 03 00 One major task of genetic studies is to construct the genetic map through linkage analysis, and then locate the genetic loci of important traits on the constructed linkage maps, identify favorable alleles which are of values to human beings, and investigate their biochemical pathways from genotype to phenotype. This book presents the linkage analysis and gene mapping methodologies, which are applicable to self-pollinated, cross-pollinated, and asexual propagated species, and genetic populations derived from two homozygous parents, two heterozygous parents, and multiple homozygous parents. Chapter 1 in this book begins with genetic mating designs and various types of genetic populations, followed by the structure of commonly used populations and analysis methods of phenotypic data. In chapters 2 and 3, estimation of recombination frequency and construction of linkage map are introduced for twenty bi-parental populations. Chapter 4 deals with two classical gene mapping methods, where no background control is considered, while chapters 5 and 6 describe the inclusive composite interval mapping (ICIM) with background control. Chapter 7 is focused on populations derived from two heterozygous parents, which can be two individuals in a random mating population, two clonal cultivars, or two single crosses from four homozygous inbred lines. Chapter 8 provides knowledge on the pure-line progeny populations derived from four to eight homozygous parents. The last two chapters covers populations, methods and commonly asked questions in genetic mapping which cannot be included previously. This book is intended for readers working on plant and animal genetics, population and quantitative genetics, and plant and animal breeding. One major task of genetic studies is to construct the genetic map through linkage analysis, and then locate the genetic loci of important traits on the constructed linkage maps, identify favorable alleles which are of values to human beings, and investigate their biochemical pathways from genotype to phenotype. This book presents the linkage analysis and gene mapping methodologies, which are applicable to self-pollinated, cross-pollinated, and asexual propagated species, and genetic populations derived from two homozygous parents, two heterozygous parents, and multiple homozygous parents. Chapter 1 in this book begins with genetic mating designs and various types of genetic populations, followed by the structure of commonly used populations and analysis methods of phenotypic data. In chapters 2 and 3, estimation of recombination frequency and construction of linkage map are introduced for twenty bi-parental populations. Chapter 4 deals with two classical gene mapping methods, where no background control is considered, while chapters 5 and 6 describe the inclusive composite interval mapping (ICIM) with background control. Chapter 7 is focused on populations derived from two heterozygous parents, which can be two individuals in a random mating population, two clonal cultivars, or two single crosses from four homozygous inbred lines. Chapter 8 provides knowledge on the pure-line progeny populations derived from four to eight homozygous parents. The last two chapters covers populations, methods and commonly asked questions in genetic mapping which cannot be included previously. This book is intended for readers working on plant and animal genetics, population and quantitative genetics, and plant and animal breeding. 02 00 This book presents the linkage analysis and gene mapping methodologies, which are applicable to self-pollinated, cross-pollinated, and asexual propagated species, and genetic populations derived from two homozygous parents, two heterozygous parents, and multiple homozygous parents. It is intended for readers working on plant and animal genetics, population and quantitative genetics, and plant and animal breeding. This book is intended for readers working on plant and animal genetics, population and quantitative genetics, and plant and animal breeding. 04 00 Preface..................................................... III<o:p></o:p>CHAPTER 1<o:p></o:p>Populations in Genetic Studies................................... 1<o:p></o:p>1.1 Commonly Used Populations in Genetic Studies ................. 2<o:p></o:p>1.1.1 Bi-Parental Populations.............................. 2<o:p></o:p>1.1.2 Multi-Parental Populations........................... 5<o:p></o:p>1.1.3 Considerations in Developing Genetic Populations .......... 9<o:p></o:p>1.2 Preliminary Analysis of Genotypic Data....................... 12<o:p></o:p>1.2.1 Collection and Coding of Genotypic Data................ 12<o:p></o:p>1.2.2 Gene Frequency and Genotypic Frequency................ 17<o:p></o:p>1.2.3 Fitness Test on Genotypic Frequencies................... 18<o:p></o:p>1.3 Genetic Effect and Genetic Variance.......................... 20<o:p></o:p>1.3.1 Calculation of Population Mean and Phenotypic Variance .... 20<o:p></o:p>1.3.2 One-Locus Additive and Dominance Model............... 23<o:p></o:p>1.3.3 Population Mean and Genetic Variance at One Locus ....... 24<o:p></o:p>1.4 ANOVA on Single Environment Trials........................ 27<o:p></o:p>1.4.1 Linear Decomposition on Phenotypic Observation .......... 27<o:p></o:p>1.4.2 Decomposition of Sum of Squares of Phenotypic Deviations ... 28<o:p></o:p>1.4.3 Single Environmental ANOVA on Rice Grain Length ........ 31<o:p></o:p>1.5 ANOVA on Multi-Environment Trials......................... 32<o:p></o:p>1.5.1 Linear Decomposition on Phenotypic Observation .......... 32<o:p></o:p>1.5.2 Decomposition of Sum of Squares of Phenotypic Deviations ... 33<o:p></o:p>1.5.3 Multi-Environmental ANOVA on Rice Grain Length ........ 38<o:p></o:p>1.6 Estimation of Genotypic Values and the Broad-Sense Heritability .... 39<o:p></o:p>1.6.1 Genotypic Values and Broad-Sense Heritability from Single Environmental Trials....................... 391.6.2 Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials....................... 411.6.3 Estimation of Genotypic Values Under Heterogeneous Error<o:p></o:p>Variances......................................... 42<o:p></o:p>Exercises................................................... 45<o:p></o:p>CHAPTER 2<o:p></o:p>Estimation of the Two-Point Recombination Frequencies ............... 51<o:p></o:p>2.1 Generation Transition Matrix............................... 51<o:p></o:p>2.1.1 Usefulness of the Transition Matrix in Linkage Analysis ...... 51<o:p></o:p>2.1.2 Transition Matrix of One Generation of Backcrossing ........ 53<o:p></o:p>2.1.3 Transition Matrix of One Generation of Selfing ............ 55<o:p></o:p>2.1.4 Transition Matrix of Doubled Haploid................... 58<o:p></o:p>2.1.5 Transition Matrix of Repeated Selfing................... 59<o:p></o:p>2.1.6 Expression of the Two-Locus Genotypic Frequencies in Matrix Format................................... 612.2 Theoretical Genotypic Frequencies at Two Loci ................. 62<o:p></o:p>2.2.1 Theoretical Frequencies of 10 Genotypes at Two Loci ....... 62<o:p></o:p>2.2.2 Theoretical Frequencies of 4 Homozygotes in Permanent Populations....................................... 652.2.3 Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations ............................652.2.4 Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations............... 692.2.5 Genotypic Frequencies of One Co-DominantLocus and One Recessive Locus in TemporaryPopulations................ 692.2.6 Genotypic Frequencies of Two DominantLoci in Temporary Populations....................................... 742.2.7 Genotypic Frequencies of One DominantLocus and One Recessive Locus in Temporary Populations................ 742.2.8 Genotypic Frequencies of Two Recessive Loci in Temporary Populations....................................... 772.3 Estimation of Two-Point Recombination Frequency .............. 77<o:p></o:p>2.3.1 Maximum Likelihood Estimation of Recombination Frequency in DH Populations.......................... 772.3.2 General Procedure on the Maximum Likelihood Estimation of Recombination Frequency.......................... 812.3.3 Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 population.... 862.3.4 Initial Values in Newton Algorithm..................... 87<o:p></o:p>2.3.5 EM Algorithm in Estimating Recombination Frequency in F2 Populations .......................................902.3.6 Effects on the Estimation of Recombination Frequency from Segregation Distortion............................... 92Exercises................................................... 95<o:p></o:p>CHAPTER 3<o:p></o:p>Three-Point Analysis and Linkage Map Construction.................. 101<o:p></o:p>3.1 Three-Point Analysis and MappingFunction.................... 102<o:p></o:p>3.1.1 Genetic Interference and Coefficient ofInterference ......... 102<o:p></o:p>3.1.2 Mapping Function.................................. 105<o:p></o:p>3.2 Construction of Genetic Linkage Maps........................ 107 3.2.1 Marker Grouping Algorithm........................... 107<o:p></o:p>3.2.2 Marker Ordering Algorithm........................... 111<o:p></o:p>3.2.3 Use of the k-Optimal Algorithm in Linkage Map Construction . 113<o:p></o:p>3.2.4 Rippling of the Ordered Markers....................... 117<o:p></o:p>3.2.5 Integration of Multiple Maps.......................... 118<o:p></o:p>3.3 Comparison of the Recombination FrequencyEstimation in Different Populations.............................................1213.3.1 LOD Score in Testing the LinkageRelationship in Different Populations....................................... 1213.3.2 Accuracy of the Estimated Recombination Frequency ........ 123<o:p></o:p>3.3.3 Least Population Size to Declare the Significant Linkage Relationship and Close Linkage........................ 1243.4 Linkage Analysis in Random Mating Populations ................ 127<o:p></o:p>3.4.1 Linkage Dis-Equilibrium in Random Mating Populations ..... 127<o:p></o:p>3.4.2 Generation Transition Matrix from Diploid Genotypes to Haploid Gametes................................. 1303.4.3 Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating.................. 132Exercises................................................... 134<o:p></o:p>CHAPTER 4<o:p></o:p>Single Marker Analysis and Simple IntervalMapping .................. 139<o:p></o:p>4.1 Single Marker Analysis.................................... 140<o:p></o:p>4.1.1 Phenotypic Means of Different Genotypes at One Marker Locus............................................1404.1.2 Single Marker Analysis by t-Test in Populations with Two Genotypes........................................ 1434.1.3 Single Marker Analysis by t-Test in Populations with Three Genotypes........................................ 1464.1.4 ANOVA in Single Marker Analysis in Populations with Three Genotypes........................................ 1504.1.5 Likelihood Ratio Test in Single Marker Analysis............ 151<o:p></o:p>4.1.6 Problems with Single Marker Analysis................... 153<o:p></o:p>4.2 Simple Interval Mapping................................... 154<o:p></o:p>4.2.1 Frequencies of the QTL Genotypes in a Marker Interval ...... 154<o:p></o:p>4.2.2 Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes.................................. 1614.2.3 Testing for the Existence of QTL....................... 166<o:p></o:p>4.2.4 Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance.............................. 1674.2.5 Applications of Simple Interval Mapping in DH and F2 Populations....................................... 1684.2.6 Phenomenon of ‘Ghost’ QTL in SimpleInterval Mapping .... 171<o:p></o:p>4.2.7 Other Problems with Simple Interval Mapping ............. 172<o:p></o:p>4.3 Threshold Values of LOD Score in QTL Mapping ................ 174 4.3.1 Significance Level and Critical Value of One Test Statistic .... 174<o:p></o:p>4.3.2 Distribution of the LRT Statistic at Single Scanning Positions in the Absence of Any QTL........................... 1764.3.3 Factors Affecting the Distribution of the Genome-Wide Largest LOD Score................................. 1774.3.4 Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping.......................... 1804.3.5 Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping................................... 184Exercises................................................... 189<o:p></o:p>CHAPTER 5<o:p></o:p>Inclusive Composite Interval Mapping............................. 195<o:p></o:p>5.1 Importance of the Control on Background Genetic Variation in QTL Mapping............................................... 1965.2 Inclusive Composite Interval Mapping in DH Populations .......... 199<o:p></o:p>5.2.1 Additive Genetic Model of One Single QTL............... 199<o:p></o:p>5.2.2 Additive Genetic Model for Multiple QTLs............... 201<o:p></o:p>5.2.3 One-Dimensional Scanning and HypothesisTesting for Additive QTLs.................................. 2025.2.4 Application of ICIM in a DH Mapping Population in Barley . . 204<o:p></o:p>5.3 Inclusive Composite Interval Mapping in F2 Populations ........... 208<o:p></o:p>5.3.1 Additive and Dominant Model of One Single QTL .......... 208<o:p></o:p>5.3.2 Additive and Dominant Model for Multiple QTLs .......... 212<o:p></o:p>5.3.3 One-Dimensional Scanning and HypothesisTesting in Additive and Dominant QTL Mapping................ 2135.3.4 Application of ICIM in an F2 Mapping Population .......... 214<o:p></o:p>5.4 Type II Error in Hypothesis Testing and Statistical Power in QTL Detection.............................................. 2165.4.1 Type II Error and Statistical Power inHypothesis Testing .... 216<o:p></o:p>5.4.2 Probability of Two Types of Error and the Appropriate Sample Size....................................... 2205.4.3 Distribution and Effect Models of QTLs Used in Power Analysis by Simulations.............................. 2225.4.4 Calculation of the Detection Power and False Discovery Rate in QTL Mapping ...................................2245.5 Comparison of IM and ICIM by Simulation.................... 230<o:p></o:p>5.5.1 QTL Detection Power and FDR from IM................. 230<o:p></o:p>5.5.2 QTL Detection Power and FDR from ICIM............... 232<o:p></o:p>5.5.3 Detection Powers Counted by Marker Intervals ............ 234<o:p></o:p>5.5.4 Suitable Population Size Required in QTLMapping ......... 235<o:p></o:p>5.6 Avoiding the Overfitting Problem in theFirst Step of Model<o:p></o:p>Selection in ICIM........................................ 237<o:p></o:p>Exercises ...................................................240CHAPTER 6<o:p></o:p>QTL Mapping for Epistasis and Genotype-by-Environment Interaction ..... 245<o:p></o:p>6.1 Epistatic QTL Mapping in DH Populations.................... 246<o:p></o:p>6.1.1 Linear Regression in Epistatic QTL Mapping and the Statistical Properties................................ 2466.1.2 Two-Dimensional Scanning on Di-GenicEpistatic QTLs ..... 248<o:p></o:p>6.1.3 Genetic Variance on Epistatic QTLs with Linkage .......... 253<o:p></o:p>6.1.4 Simulation Study on Epistatic QTL Mapping in DH Populations....................................... 2546.2 Epistatic QTL Mapping in F2 Populations..................... 257<o:p></o:p>6.2.1 The Di-Genic Epistasis Model in F2 Populations ........... 257<o:p></o:p>6.2.2 Epistatic QTL Mapping Procedure in F2 Population ........ 258<o:p></o:p>6.2.3 Detection Power of Epistatic QTLs in F2Populations ....... 265<o:p></o:p>6.3 Genetic Analysis and Detection Power of the Most Common Di-Genic Interactions..................................... 2686.3.1 Genetic Effects in Di-Genic Interactions.................. 268<o:p></o:p>6.3.2 Decomposition of Genetic Variance at the Presence of Di-Genic Epistasis................................ 2706.3.3 Power Simulation of Epistatic QTL Mapping.............. 276<o:p></o:p>6.3.4 Issues in Epistatic QTL Mapping....................... 281<o:p></o:p>6.4 Mapping of the QTL by Environment Interactions ............... 282<o:p></o:p>6.4.1 Mapping of the Additive QTL byEnvironment Interactions ... 282<o:p></o:p>6.4.2 Mapping of the Epistatic QTL and Environment Interactions . 285<o:p></o:p>6.4.3 QTL and Environment Interactions in One Actual RIL<o:p></o:p>Population in Maize................................. 287<o:p></o:p>Exercises................................................... 291<o:p></o:p>CHAPTER 7<o:p></o:p>Genetic Analysis in Hybrid F1 of TwHeterozygous Parents and Double-Cross F1 of Four Homozygous Parents.................... 2957.1 Linage Analysis in the Hybrid F1 Derivedfrom Two Heterozygous Parents................................................ 2967.1.1 Categories of Polymorphism Markers ....................296<o:p></o:p>7.1.2 Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci.......... 2987.1.3 Estimation of the Recombination Frequency Between Two Fully-Informative Markers............................ 2997.1.4 Haploid Type Rebuilding in theHeterozygous Parents ....... 302<o:p></o:p>7.2 Estimation of the Recombination Frequencfor Incompletely Informative Markers...................................... 3057.2.1 Theoretical Frequencies of Identifiable Genotypes Between the Complete Marker and Other Three Categoriesof Markers . 3067.2.2 Theoretical Frequencies of Identifiable Genotypes Between Two Markers Belonging to Category II, III, or IV .......... 3087.2.3 Theoretical Frequencies of Identifiable Genotypes Between Two Category IV Markers............................ 3117.2.4 Haploid Type Rebuilding at the Presence of All Categories of Markers........................................ 3167.3 Linkage Analysis in Double Cross F1 Derived from Four Pure-Line Parents................................................ 3197.3.1 Marker Categories and Estimation of Recombination Frequency in the Double Cross F1 Population............. 3197.3.2 Equivalence Between the Double Cross F1of Pure-Line Parents and Hybrid F1 of Heterozygous Parents............ 3237.3.3 Genotypic Frequencies at Three Complete Markers ......... 325<o:p></o:p>7.3.4 Imputation of Incomplete and Missing Marker Information ... 327<o:p></o:p>7.4 QTL Mapping in the Double Cross F1Population Derived from Four Pure-Line Parents........................................ 3317.4.1 One-QTL Genetic Model in Double Cross F1 Population ..... 332<o:p></o:p>7.4.2 The Linear Regression Model of the Phenotype on Marker Type for Multiple QTLs.............................. 3357.4.3 Inclusive Composite Interval Mapping(ICIM) in the Double Cross F1 Population................................. 336<o:p></o:p>Exercises................................................... 338<o:p></o:p>CHAPTER 8<o:p></o:p>Genetic Analysis in Multi-Parental Pure-LineProgeny Populations........ 345<o:p></o:p>8.1 Linkage Analysis in Four-Parental Pure-LinePopulations .......... 346<o:p></o:p>8.1.1 Development Procedure and Marker Classification in Four-Parental Pure-Line Populations.................. 3468.1.2 Theoretical Frequencies of Genotypes and Estimation of Recombination Frequency at Two Complete Loci......... 3488.1.3 Estimation of the Recombination Frequency Involving Incomplete Markers................................. 3558.1.4 Situations When Number of Inbred Parents Smaller Than Four.............................................3598.2 Linkage Analysis in Eight-Parental Pure-Line Populations ......... 360<o:p></o:p>8.2.1 Development Procedure and Marker Classification in Eight-Parental Pure-Line Populations................. 3608.2.2 Marker Classification and Genotypic Coding in Eight-Parental Pure-Line Populations................. 3628.2.3 Theoretical Frequencies of Genotypes atTwo Complete Loci . . 363<o:p></o:p>8.2.4 Estimation of the Recombination Frequency Between Any Two Categories ofMarkers............................ 3688.2.5 Situations When the Number of Inbred Parents Smaller Than Eight............................................ 3708.3 QTL Mapping in Four-Parental Pure-LinePopulations ............ 370<o:p></o:p>8.3.1 Genetic Constitution at Three CompleteLoci ............. 371<o:p></o:p>8.3.2 Imputation of the Incomplete and Missing Marker Information....................................... 3728.3.3 The Linear Regression Model of Phenotype on Marker Types. . 378<o:p></o:p>8.3.4 Inclusive Composite Interval Mapping(ICIM) in Four-Parental Pure-Line Populations.................. 3808.4 QTL Mapping in Eight-Parental Pure-Line Populations ........... 383<o:p></o:p>8.4.1 Genetic Constitution at Three CompleteLoci ............. 383<o:p></o:p>8.4.2 The Linear Regression Model of Phenotypeon Marker Types. . 389<o:p></o:p>8.4.3 Inclusive Composite Interval Mapping(ICIM) in Eight-Parental Pure-Line Populations................. 391Exercises................................................... 394<o:p></o:p>CHAPTER 9<o:p></o:p>QTL Mapping in Other Genetic Populations........................ 399<o:p></o:p>9.1 Selective Genotyping Analysis and Bulked Segregant Analysis....... 400<o:p></o:p>9.1.1 Statistical Principles of Selective Genotyping Analysis ....... 400<o:p></o:p>9.1.2 Likelihood Ratio Test and LOD Score Statistics from Selective Genotyping Analysis................................ 4029.1.3 Bulked Segregant Analysis............................ 403<o:p></o:p>9.1.4 Problems with Selective Genotyping Analysis and Bulked Segregant Analysis.................................. 4049.2 QTL Mapping in Populations of Chromosomal Segment Substitution Lines..................................................4049.2.1 Characteristics of Chromosomal Segment Substitution Lines . . 404<o:p></o:p>9.2.2 Mapping Methods in Populations of Chromosomal Segment Substitution Lines.................................. 4079.2.3 QTL Mapping for Grain Length in a CSSLPopulation in Rice........................................... 4129.3 QTL Mapping in Genetic Populations of Multiple Parents Crossed with One Common Parent................................. 4149.3.1 Generalized Linear Regression and Model Selection ......... 415<o:p></o:p>9.3.2 Parameter Estimation and HypothesisTesting in JICIM ..... 415<o:p></o:p>9.3.3 QTL Mapping for Flowering Time in an Arabidopsis NAM Population........................................ 4179.4 Mendelization of Quantitative Trait Genes..................... 419<o:p></o:p>9.4.1 Preliminary Mapping of One QTL on GrainWidth of Rice in One RIL Population................................. 4209.4.2 Validation of the Grain Width QTL byChromosomal Segment Substitution Lines........................... 4219.4.3 Mendelization of a Stable QTL on Grain Width ............ 424<o:p></o:p>9.4.4 Fine Mapping and Functional Analysis of the Gene at a Stable Grain Width QTL.................................. 4259.5 Association Mapping in Natural Populations.................... 427<o:p></o:p>9.5.1 Linkage Disequilibrium is the Prerequisite of Gene Mapping ... 427<o:p></o:p>9.5.2 Linkage Disequilibrium in Random Mating Populations ...... 4299.5.3 Factors Influencing Linkage Disequilibrium ............... 432<o:p></o:p>9.5.4 Comparison of Linkage and Association Approaches in Gene<o:p></o:p>Mapping......................................... 435<o:p></o:p>Exercises................................................... 439<o:p></o:p>CHAPTER 10<o:p></o:p>More on the Frequently Asked Questions in QTLMapping .............. 443<o:p></o:p>10.1 Genetic Variance and Contribution to Phenotypic Variation of the Detected QTL.......................................... 44310.1.1 Genetic Variance and Phenotypic Contribution from One QTL ..........................................44310.1.2 Genetic Variance and PhenotypicContribution of Linked QTLs ..........................................44510.1.3 Phenotypic Contribution and the QTL Detection Power.... 448<o:p></o:p>10.2 On the Use of Composite Traits in QTL Mapping ............... 450<o:p></o:p>10.2.1 Composite Traits and Their Applications in Genetic Studies and Breeding.............................. 45010.2.2 QTL Mapping on Component and Composite Traits in One Maize RIL Population............................. 45110.2.3 Genetic Effects and Genetic Variances on Composite Traits . 455<o:p></o:p>10.2.4 Power Analysis in QTL Mapping on Composite Traits ..... 461<o:p></o:p>10.2.5 Heritability of Composite Traits...................... 465<o:p></o:p>10.3 Effects on QTL Detection by the Increasein Marker Density ....... 470<o:p></o:p>10.3.1 Effects of Denser Markers on Independen tQTLs ......... 470<o:p></o:p>10.3.2 Effect of Denser Markers on Linked QTLs.............. 471<o:p></o:p>10.4 Imputation of Missing Marker Types and Their Effects in QTL Mapping in Bi-Parental Populations......................... 47410.4.1 Imputation of Missing and Incomplete Marker Types ...... 474<o:p></o:p>10.4.2 QTLs on Plant Height in an F2 Population in Rice ........ 477<o:p></o:p>10.4.3 Effects of Missing Marker Types on QTLDetection ....... 479<o:p></o:p>10.5 Effects of Segregation Distortion on Genetic Studies ............. 481<o:p></o:p>10.5.1 Segregation Distortion Loci in One Rice F2 Population ..... 481<o:p></o:p>10.5.2 Effects of Segregation Distortion on QTL Mapping in Populations with Three Genotypes at Each Locus ...... 48210.5.3 Genetic Distance That can be Affected by Segregation Distortion.......................................48610.5.4 Effects of Segregation Distortion on QTLMapping in Populations with Two Genotypes at Each Locus....... 48710.6 Non-Normality of the Phenotypic Distribution ................. 488<o:p></o:p>10.6.1 Phenotypic Model and Distribution of Quantitative Traits . . 488<o:p></o:p>10.6.2 QTL Mapping on Phenotypic Traits of the Non-Normal<o:p></o:p>Distributions.................................... 489<o:p></o:p>Exercises................................................... 492<o:p></o:p>References.................................................. 495<o:p></o:p>Index...................................................... 503<o:p></o:p>Appendix A: Journal Articles Making Up ThisBook .................. 509<o:p></o:p>Appendix B: Dissertations of Post-GraduatesMaking Up This Book ...... 513<o:p></o:p>Appendix C: Integrated Software Packages MakingUp This Book ........ 515<o:p></o:p> Preface..................................................... III<o:p></o:p>CHAPTER 1<o:p></o:p>Populations in Genetic Studies................................... 1<o:p></o:p>1.1 Commonly Used Populations in GeneticStudies ................. 2<o:p></o:p>1.1.1 Bi-Parental Populations.............................. 2<o:p></o:p>1.1.2 Multi-Parental Populations........................... 5<o:p></o:p>1.1.3 Considerations in Developing GeneticPopulations .......... 9<o:p></o:p>1.2 Preliminary Analysis of Genotypic Data....................... 12<o:p></o:p>1.2.1 Collection and Coding of Genotypic Data................ 12<o:p></o:p>1.2.2 Gene Frequency and Genotypic Frequency................ 17<o:p></o:p>1.2.3 Fitness Test on Genotypic Frequencies................... 18<o:p></o:p>1.3 Genetic Effect and Genetic Variance.......................... 20<o:p></o:p>1.3.1 Calculation of Population Mean andPhenotypic Variance .... 20<o:p></o:p>1.3.2 One-Locus Additive and Dominance Model............... 23<o:p></o:p>1.3.3 Population Mean and Genetic Variance atOne Locus ....... 24<o:p></o:p>1.4 ANOVA on Single Environment Trials........................ 27<o:p></o:p>1.4.1 Linear Decomposition on PhenotypicObservation .......... 27<o:p></o:p>1.4.2 Decomposition of Sum of Squares ofPhenotypic Deviations ... 28<o:p></o:p>1.4.3 Single Environmental ANOVA on Rice GrainLength ........ 31<o:p></o:p>1.5 ANOVA on Multi-Environment Trials......................... 32<o:p></o:p>1.5.1 Linear Decomposition on PhenotypicObservation .......... 32<o:p></o:p>1.5.2 Decomposition of Sum of Squares ofPhenotypic Deviations ... 33<o:p></o:p>1.5.3 Multi-Environmental ANOVA on Rice GrainLength ........ 38<o:p></o:p>1.6 Estimation of Genotypic Values and theBroad-Sense Heritability .... 39<o:p></o:p>1.6.1 Genotypic Values and Broad-SenseHeritability<o:p></o:p>from Single Environmental Trials....................... 39<o:p></o:p>1.6.2 Genotypic Values and Broad-Sense Heritability<o:p></o:p>from Multi-Environmental Trials....................... 41<o:p></o:p>1.6.3 Estimation of Genotypic Values UnderHeterogeneous Error<o:p></o:p>Variances......................................... 42<o:p></o:p>Exercises................................................... 45<o:p></o:p>CHAPTER 2<o:p></o:p>Estimation of the Two-Point RecombinationFrequencies ............... 51<o:p></o:p>2.1 Generation Transition Matrix............................... 51<o:p></o:p>2.1.1 Usefulness of the Transition Matrix inLinkage Analysis ...... 51<o:p></o:p>2.1.2 Transition Matrix of One Generation ofBackcrossing ........ 53<o:p></o:p>2.1.3 Transition Matrix of One Generation ofSelfing ............ 55<o:p></o:p>2.1.4 Transition Matrix of Doubled Haploid................... 58<o:p></o:p>2.1.5 Transition Matrix of Repeated Selfing................... 59<o:p></o:p>2.1.6 Expression of the Two-Locus GenotypicFrequencies<o:p></o:p>in Matrix Format................................... 61<o:p></o:p>2.2 Theoretical Genotypic Frequencies at TwoLoci ................. 62<o:p></o:p>2.2.1 Theoretical Frequencies of 10 Genotypesat Two Loci ....... 62<o:p></o:p>2.2.2 Theoretical Frequencies of 4 Homozygotesin Permanent<o:p></o:p>Populations....................................... 65<o:p></o:p>2.2.3 Genotypic Frequencies of Two Co-DominantLoci<o:p></o:p>in Temporary Populations ............................65<o:p></o:p>2.2.4 Genotypic Frequencies of One Co-DominantLocus and One<o:p></o:p>Dominant Locus in Temporary Populations............... 69<o:p></o:p>2.2.5 Genotypic Frequencies of One Co-DominantLocus and One<o:p></o:p>Recessive Locus in TemporaryPopulations................ 69<o:p></o:p>2.2.6 Genotypic Frequencies of Two DominantLoci in Temporary<o:p></o:p>Populations....................................... 74<o:p></o:p>2.2.7 Genotypic Frequencies of One DominantLocus and One<o:p></o:p>Recessive Locus in TemporaryPopulations................ 74<o:p></o:p>2.2.8 Genotypic Frequencies of Two RecessiveLoci in Temporary<o:p></o:p>Populations....................................... 77<o:p></o:p>2.3 Estimation of Two-Point RecombinationFrequency .............. 77<o:p></o:p>2.3.1 Maximum Likelihood Estimation ofRecombination<o:p></o:p>Frequency in DHPopulations.......................... 77<o:p></o:p>2.3.2 General Procedure on the MaximumLikelihood Estimation<o:p></o:p>of Recombination Frequency.......................... 81<o:p></o:p>2.3.3 Estimation of Recombination FrequencyBetween One<o:p></o:p>Co-Dominant and One Dominant Marker in F2population.... 86<o:p></o:p>2.3.4 Initial Values in Newton Algorithm..................... 87<o:p></o:p>2.3.5 EM Algorithm in Estimating RecombinationFrequency in F2<o:p></o:p>Populations .......................................90<o:p></o:p>2.3.6 Effects on the Estimation ofRecombination Frequency from<o:p></o:p>Segregation Distortion............................... 92<o:p></o:p>Exercises................................................... 95<o:p></o:p>CHAPTER 3<o:p></o:p>Three-Point Analysis and Linkage Map Construction.................. 101<o:p></o:p>3.1 Three-Point Analysis and MappingFunction.................... 102<o:p></o:p>3.1.1 Genetic Interference and Coefficient ofInterference ......... 102<o:p></o:p>3.1.2 Mapping Function.................................. 105<o:p></o:p>VI Contents<o:p></o:p>3.2 Construction of Genetic Linkage Maps........................ 107<o:p></o:p>3.2.1 Marker GroupingAlgorithm........................... 107<o:p></o:p>3.2.2 Marker Ordering Algorithm........................... 111<o:p></o:p>3.2.3 Use of the k-Optimal Algorithm in LinkageMap Construction . 113<o:p></o:p>3.2.4 Rippling of the Ordered Markers....................... 117<o:p></o:p>3.2.5 Integration of Multiple Maps.......................... 118<o:p></o:p>3.3 Comparison of the Recombination FrequencyEstimation in Different<o:p></o:p>Populations.............................................121<o:p></o:p>3.3.1 LOD Score in Testing the LinkageRelationship in Different<o:p></o:p>Populations....................................... 121<o:p></o:p>3.3.2 Accuracy of the Estimated RecombinationFrequency ........ 123<o:p></o:p>3.3.3 Least Population Size to Declare theSignificant Linkage<o:p></o:p>Relationship and Close Linkage........................ 124<o:p></o:p>3.4 Linkage Analysis in Random MatingPopulations ................ 127<o:p></o:p>3.4.1 Linkage Dis-Equilibrium in Random MatingPopulations ..... 127<o:p></o:p>3.4.2 Generation Transition Matrix from DiploidGenotypes<o:p></o:p>to Haploid Gametes................................. 130<o:p></o:p>3.4.3 Gametic and Genotypic Frequencies inPopulations After<o:p></o:p>Several Generations of Random Mating.................. 132<o:p></o:p>Exercises................................................... 134<o:p></o:p>CHAPTER 4<o:p></o:p>Single Marker Analysis and Simple IntervalMapping .................. 139<o:p></o:p>4.1 Single Marker Analysis.................................... 140<o:p></o:p>4.1.1 Phenotypic Means of Different Genotypesat One Marker<o:p></o:p>Locus............................................140<o:p></o:p>4.1.2 Single Marker Analysis by t-Test inPopulations with Two<o:p></o:p>Genotypes........................................ 143<o:p></o:p>4.1.3 Single Marker Analysis by t-Test inPopulations with Three<o:p></o:p>Genotypes........................................ 146<o:p></o:p>4.1.4 ANOVA in Single Marker Analysis inPopulations with Three<o:p></o:p>Genotypes........................................ 150<o:p></o:p>4.1.5 Likelihood Ratio Test in Single MarkerAnalysis............ 151<o:p></o:p>4.1.6 Problems with Single Marker Analysis................... 153<o:p></o:p>4.2 Simple Interval Mapping................................... 154<o:p></o:p>4.2.1 Frequencies of the QTL Genotypes in aMarker Interval ...... 154<o:p></o:p>4.2.2 Maximum Likelihood Estimation ofPhenotypic Means<o:p></o:p>of QTL Genotypes.................................. 161<o:p></o:p>4.2.3 Testing for the Existence of QTL....................... 166<o:p></o:p>4.2.4 Estimation of Genetic Effects of QTL andIts Contribution<o:p></o:p>to Phenotypic Variance.............................. 167<o:p></o:p>4.2.5 Applications of Simple Interval Mappingin DH and F2<o:p></o:p>Populations....................................... 168<o:p></o:p>4.2.6 Phenomenon of ‘Ghost’ QTL in SimpleInterval Mapping .... 171<o:p></o:p>4.2.7 Other Problems with Simple IntervalMapping ............. 172<o:p></o:p>Contents VII<o:p></o:p>4.3 Threshold Values of LOD Score in QTLMapping ................ 174<o:p></o:p>4.3.1 Significance Level and Critical Value ofOne Test Statistic .... 174<o:p></o:p>4.3.2 Distribution of the LRT Statistic at SingleScanning Positions<o:p></o:p>in the Absence of Any QTL........................... 176<o:p></o:p>4.3.3 Factors Affecting the Distribution of theGenome-Wide<o:p></o:p>Largest LOD Score................................. 177<o:p></o:p>4.3.4 Number of Effective Tests and theEmpirical LOD Score<o:p></o:p>Thresholds in QTL Mapping.......................... 180<o:p></o:p>4.3.5 Permutation Test and the Empirical LODScore Thresholds<o:p></o:p>in QTL Mapping................................... 184<o:p></o:p>Exercises................................................... 189<o:p></o:p>CHAPTER 5<o:p></o:p>Inclusive Composite Interval Mapping............................. 195<o:p></o:p>5.1 Importance of the Control on BackgroundGenetic Variation in QTL<o:p></o:p>Mapping............................................... 196<o:p></o:p>5.2 Inclusive Composite Interval Mapping in DHPopulations .......... 199<o:p></o:p>5.2.1 Additive Genetic Model of One Single QTL............... 199<o:p></o:p>5.2.2 Additive Genetic Model for Multiple QTLs............... 201<o:p></o:p>5.2.3 One-Dimensional Scanning and HypothesisTesting<o:p></o:p>for Additive QTLs.................................. 202<o:p></o:p>5.2.4 Application of ICIM in a DH MappingPopulation in Barley . . 204<o:p></o:p>5.3 Inclusive Composite Interval Mapping in F2Populations ........... 208<o:p></o:p>5.3.1 Additive and Dominant Model of One SingleQTL .......... 208<o:p></o:p>5.3.2 Additive and Dominant Model for MultipleQTLs .......... 212<o:p></o:p>5.3.3 One-Dimensional Scanning and HypothesisTesting<o:p></o:p>in Additive and Dominant QTL Mapping................ 213<o:p></o:p>5.3.4 Application of ICIM in an F2 MappingPopulation .......... 214<o:p></o:p>5.4 Type II Error in Hypothesis Testing andStatistical Power in QTL<o:p></o:p>Detection.............................................. 216<o:p></o:p>5.4.1 Type II Error and Statistical Power inHypothesis Testing .... 216<o:p></o:p>5.4.2 Probability of Two Types of Error and theAppropriate<o:p></o:p>Sample Size....................................... 220<o:p></o:p>5.4.3 Distribution and Effect Models of QTLsUsed in Power<o:p></o:p>Analysis by Simulations.............................. 222<o:p></o:p>5.4.4 Calculation of the Detection Power andFalse Discovery Rate<o:p></o:p>in QTL Mapping ...................................224<o:p></o:p>5.5 Comparison of IM and ICIM by Simulation.................... 230<o:p></o:p>5.5.1 QTL Detection Power and FDR from IM................. 230<o:p></o:p>5.5.2 QTL Detection Power and FDR from ICIM............... 232<o:p></o:p>5.5.3 Detection Powers Counted by MarkerIntervals ............ 234<o:p></o:p>5.5.4 Suitable Population Size Required in QTLMapping ......... 235<o:p></o:p>5.6 Avoiding the Overfitting Problem in theFirst Step of Model<o:p></o:p>Selection in ICIM........................................ 237<o:p></o:p>Exercises ...................................................240<o:p></o:p>VIII Contents<o:p></o:p>CHAPTER 6<o:p></o:p>QTL Mapping for Epistasis andGenotype-by-Environment Interaction ..... 245<o:p></o:p>6.1 Epistatic QTL Mapping in DH Populations.................... 246<o:p></o:p>6.1.1 Linear Regression in Epistatic QTLMapping and the<o:p></o:p>Statistical Properties................................ 246<o:p></o:p>6.1.2 Two-Dimensional Scanning on Di-GenicEpistatic QTLs ..... 248<o:p></o:p>6.1.3 Genetic Variance on Epistatic QTLs withLinkage .......... 253<o:p></o:p>6.1.4 Simulation Study on Epistatic QTL Mappingin DH<o:p></o:p>Populations....................................... 254<o:p></o:p>6.2 Epistatic QTL Mapping in F2 Populations..................... 257<o:p></o:p>6.2.1 The Di-Genic Epistasis Model in F2Populations ........... 257<o:p></o:p>6.2.2 Epistatic QTL Mapping Procedure in F2Population ........ 258<o:p></o:p>6.2.3 Detection Power of Epistatic QTLs in F2Populations ....... 265<o:p></o:p>6.3 Genetic Analysis and Detection Power of theMost Common<o:p></o:p>Di-Genic Interactions..................................... 268<o:p></o:p>6.3.1 Genetic Effects in Di-Genic Interactions.................. 268<o:p></o:p>6.3.2 Decomposition of Genetic Variance at thePresence<o:p></o:p>of Di-Genic Epistasis................................ 270<o:p></o:p>6.3.3 Power Simulation of Epistatic QTL Mapping.............. 276<o:p></o:p>6.3.4 Issues in Epistatic QTL Mapping....................... 281<o:p></o:p>6.4 Mapping of the QTL by EnvironmentInteractions ............... 282<o:p></o:p>6.4.1 Mapping of the Additive QTL byEnvironment Interactions ... 282<o:p></o:p>6.4.2 Mapping of the Epistatic QTL andEnvironment Interactions . 285<o:p></o:p>6.4.3 QTL and Environment Interactions in OneActual RIL<o:p></o:p>Population in Maize................................. 287<o:p></o:p>Exercises................................................... 291<o:p></o:p>CHAPTER 7<o:p></o:p>Genetic Analysis in Hybrid F1 of TwoHeterozygous Parents<o:p></o:p>and Double-Cross F1 of Four Homozygous Parents.................... 295<o:p></o:p>7.1 Linage Analysis in the Hybrid F1 Derivedfrom Two Heterozygous<o:p></o:p>Parents................................................ 296<o:p></o:p>7.1.1 Categories of Polymorphism Markers ....................296<o:p></o:p>7.1.2 Unknown Linkage Phases in HeterozygousParents<o:p></o:p>and Genotypes in Their F1 Progenies at Two Loci.......... 298<o:p></o:p>7.1.3 Estimation of the Recombination FrequencyBetween Two<o:p></o:p>Fully-Informative Markers............................ 299<o:p></o:p>7.1.4 Haploid Type Rebuilding in theHeterozygous Parents ....... 302<o:p></o:p>7.2 Estimation of the Recombination Frequencyfor Incompletely<o:p></o:p>Informative Markers...................................... 305<o:p></o:p>7.2.1 Theoretical Frequencies of IdentifiableGenotypes Between<o:p></o:p>the Complete Marker and Other Three Categoriesof Markers . 306<o:p></o:p>7.2.2 Theoretical Frequencies of IdentifiableGenotypes Between<o:p></o:p>Two Markers Belonging to Category II, III, orIV .......... 308<o:p></o:p>Contents IX<o:p></o:p>7.2.3 Theoretical Frequencies of IdentifiableGenotypes Between<o:p></o:p>Two Category IV Markers............................ 311<o:p></o:p>7.2.4 Haploid Type Rebuilding at the Presenceof All Categories<o:p></o:p>of Markers........................................ 316<o:p></o:p>7.3 Linkage Analysis in Double Cross F1 Derivedfrom Four Pure-Line<o:p></o:p>Parents................................................ 319<o:p></o:p>7.3.1 Marker Categories and Estimation ofRecombination<o:p></o:p>Frequency in the Double Cross F1 Population............. 319<o:p></o:p>7.3.2 Equivalence Between the Double Cross F1of Pure-Line<o:p></o:p>Parents and Hybrid F1 of Heterozygous Parents............ 323<o:p></o:p>7.3.3 Genotypic Frequencies at Three CompleteMarkers ......... 325<o:p></o:p>7.3.4 Imputation of Incomplete and MissingMarker Information ... 327<o:p></o:p>7.4 QTL Mapping in the Double Cross F1Population Derived from Four<o:p></o:p>Pure-Line Parents........................................ 331<o:p></o:p>7.4.1 One-QTL Genetic Model in Double Cross F1Population ..... 332<o:p></o:p>7.4.2 The Linear Regression Model of thePhenotype on Marker<o:p></o:p>Type for MultipleQTLs.............................. 335<o:p></o:p>7.4.3 Inclusive Composite Interval Mapping(ICIM) in the Double<o:p></o:p>Cross F1 Population................................. 336<o:p></o:p>Exercises................................................... 338<o:p></o:p>CHAPTER 8<o:p></o:p>Genetic Analysis in Multi-Parental Pure-LineProgeny Populations........ 345<o:p></o:p>8.1 Linkage Analysis in Four-Parental Pure-LinePopulations .......... 346<o:p></o:p>8.1.1 Development Procedure and MarkerClassification<o:p></o:p>in Four-Parental Pure-Line Populations.................. 346<o:p></o:p>8.1.2 Theoretical Frequencies of Genotypes andEstimation<o:p></o:p>of Recombination Frequency at Two Complete Loci......... 348<o:p></o:p>8.1.3 Estimation of the Recombination FrequencyInvolving<o:p></o:p>Incomplete Markers................................. 355<o:p></o:p>8.1.4 Situations When Number of Inbred ParentsSmaller Than<o:p></o:p>Four.............................................359<o:p></o:p>8.2 Linkage Analysis in Eight-ParentalPure-Line Populations ......... 360<o:p></o:p>8.2.1 Development Procedure and MarkerClassification<o:p></o:p>in Eight-Parental Pure-Line Populations................. 360<o:p></o:p>8.2.2 Marker Classification and GenotypicCoding<o:p></o:p>in Eight-Parental Pure-Line Populations................. 362<o:p></o:p>8.2.3 Theoretical Frequencies of Genotypes atTwo Complete Loci . . 363<o:p></o:p>8.2.4 Estimation of the Recombination FrequencyBetween Any<o:p></o:p>Two Categories ofMarkers............................ 368<o:p></o:p>8.2.5 Situations When the Number of InbredParents Smaller Than<o:p></o:p>Eight............................................ 370<o:p></o:p>8.3 QTL Mapping in Four-Parental Pure-LinePopulations ............ 370<o:p></o:p>8.3.1 Genetic Constitution at Three CompleteLoci ............. 371<o:p></o:p>X Contents<o:p></o:p>8.3.2 Imputation of the Incomplete and MissingMarker<o:p></o:p>Information....................................... 372<o:p></o:p>8.3.3 The Linear Regression Model of Phenotype onMarker Types. . 378<o:p></o:p>8.3.4 Inclusive Composite Interval Mapping(ICIM)<o:p></o:p>in Four-Parental Pure-Line Populations.................. 380<o:p></o:p>8.4 QTL Mapping in Eight-Parental Pure-LinePopulations ........... 383<o:p></o:p>8.4.1 Genetic Constitution at Three CompleteLoci ............. 383<o:p></o:p>8.4.2 The Linear Regression Model of Phenotypeon Marker Types. . 389<o:p></o:p>8.4.3 Inclusive Composite Interval Mapping(ICIM)<o:p></o:p>in Eight-Parental Pure-Line Populations................. 391<o:p></o:p>Exercises................................................... 394<o:p></o:p>CHAPTER 9<o:p></o:p>QTL Mapping in Other Genetic Populations........................ 399<o:p></o:p>9.1 Selective Genotyping Analysis and BulkedSegregant Analysis....... 400<o:p></o:p>9.1.1 Statistical Principles of SelectiveGenotyping Analysis ....... 400<o:p></o:p>9.1.2 Likelihood Ratio Test and LOD ScoreStatistics from Selective<o:p></o:p>Genotyping Analysis................................ 402<o:p></o:p>9.1.3 Bulked Segregant Analysis............................ 403<o:p></o:p>9.1.4 Problems with Selective GenotypingAnalysis and Bulked<o:p></o:p>Segregant Analysis.................................. 404<o:p></o:p>9.2 QTL Mapping in Populations of ChromosomalSegment Substitution<o:p></o:p>Lines..................................................404<o:p></o:p>9.2.1 Characteristics of Chromosomal SegmentSubstitution Lines . . 404<o:p></o:p>9.2.2 Mapping Methods in Populations ofChromosomal Segment<o:p></o:p>Substitution Lines.................................. 407<o:p></o:p>9.2.3 QTL Mapping for Grain Length in a CSSLPopulation<o:p></o:p>in Rice........................................... 412<o:p></o:p>9.3 QTL Mapping in Genetic Populations ofMultiple Parents Crossed<o:p></o:p>with One Common Parent................................. 414<o:p></o:p>9.3.1 Generalized Linear Regression and ModelSelection ......... 415<o:p></o:p>9.3.2 Parameter Estimation and HypothesisTesting in JICIM ..... 415<o:p></o:p>9.3.3 QTL Mapping for Flowering Time in anArabidopsis NAM<o:p></o:p>Population........................................ 417<o:p></o:p>9.4 Mendelization of Quantitative Trait Genes..................... 419<o:p></o:p>9.4.1 Preliminary Mapping of One QTL on GrainWidth of Rice in<o:p></o:p>One RIL Population................................. 420<o:p></o:p>9.4.2 Validation of the Grain Width QTL byChromosomal<o:p></o:p>Segment Substitution Lines........................... 421<o:p></o:p>9.4.3 Mendelization of a Stable QTL on GrainWidth ............ 424<o:p></o:p>9.4.4 Fine Mapping and Functional Analysis ofthe Gene at a Stable<o:p></o:p>Grain Width QTL.................................. 425<o:p></o:p>9.5 Association Mapping in NaturalPopulations.................... 427<o:p></o:p>9.5.1 Linkage Disequilibrium is thePrerequisite of Gene Mapping ... 427<o:p></o:p>9.5.2 Linkage Disequilibrium in Random MatingPopulations ...... 429<o:p></o:p>Contents XI<o:p></o:p>9.5.3 Factors Influencing LinkageDisequilibrium ............... 432<o:p></o:p>9.5.4 Comparison of Linkage and AssociationApproaches in Gene<o:p></o:p>Mapping......................................... 435<o:p></o:p>Exercises................................................... 439<o:p></o:p>CHAPTER 10<o:p></o:p>More on the Frequently Asked Questions in QTLMapping .............. 443<o:p></o:p>10.1 Genetic Variance and Contribution toPhenotypic Variation of the<o:p></o:p>Detected QTL.......................................... 443<o:p></o:p>10.1.1 Genetic Variance and PhenotypicContribution from One<o:p></o:p>QTL ..........................................443<o:p></o:p>10.1.2 Genetic Variance and PhenotypicContribution of Linked<o:p></o:p>QTLs ..........................................445<o:p></o:p>10.1.3 Phenotypic Contribution and the QTLDetection Power.... 448<o:p></o:p>10.2 On the Use of Composite Traits in QTLMapping ............... 450<o:p></o:p>10.2.1 Composite Traits and Their Applicationsin Genetic<o:p></o:p>Studies and Breeding.............................. 450<o:p></o:p>10.2.2 QTL Mapping on Component and CompositeTraits in One<o:p></o:p>Maize RIL Population............................. 451<o:p></o:p>10.2.3 Genetic Effects and Genetic Variances onComposite Traits . 455<o:p></o:p>10.2.4 Power Analysis in QTL Mapping onComposite Traits ..... 461<o:p></o:p>10.2.5 Heritability of Composite Traits...................... 465<o:p></o:p>10.3 Effects on QTL Detection by the Increasein Marker Density ....... 470<o:p></o:p>10.3.1 Effects of Denser Markers on IndependentQTLs ......... 470<o:p></o:p>10.3.2 Effect of Denser Markers on Linked QTLs.............. 471<o:p></o:p>10.4 Imputation of Missing Marker Types and TheirEffects in QTL<o:p></o:p>Mapping in Bi-Parental Populations......................... 474<o:p></o:p>10.4.1 Imputation of Missing and IncompleteMarker Types ...... 474<o:p></o:p>10.4.2 QTLs on Plant Height in an F2 Populationin Rice ........ 477<o:p></o:p>10.4.3 Effects of Missing Marker Types on QTLDetection ....... 479<o:p></o:p>10.5 Effects of Segregation Distortion onGenetic Studies ............. 481<o:p></o:p>10.5.1 Segregation Distortion Loci in One RiceF2 Population ..... 481<o:p></o:p>10.5.2 Effects of Segregation Distortion on QTLMapping<o:p></o:p>in Populations with Three Genotypes at EachLocus ...... 482<o:p></o:p>10.5.3 Genetic Distance That can be Affected bySegregation<o:p></o:p>Distortion.......................................486<o:p></o:p>10.5.4 Effects of Segregation Distortion on QTLMapping<o:p></o:p>in Populations with Two Genotypes at Each Locus....... 487<o:p></o:p>10.6 Non-Normality of the PhenotypicDistribution ................. 488<o:p></o:p>10.6.1 Phenotypic Model and Distribution ofQuantitative Traits . . 488<o:p></o:p>10.6.2 QTL Mapping on Phenotypic Traits of theNon-Normal<o:p></o:p>Distributions.................................... 489<o:p></o:p>Exercises................................................... 492<o:p></o:p>References.................................................. 495<o:p></o:p>Index...................................................... 503<o:p></o:p>Appendix A: Journal Articles Making Up ThisBook .................. 509<o:p></o:p>Appendix B: Dissertations of Post-GraduatesMaking Up This Book ...... 513<o:p></o:p>Appendix C: Integrated Software Packages MakingUp This Book ........ 515<o:p></o:p> 21 00 06 01 https://laboutique.edpsciences.fr/produit/1344/9782759830435/linkage-analysis-and-gene-mapping 01 00 03 02 https://laboutique.edpsciences.fr/system/product_pictures/data/009/982/947/original/9782759830428-Linkage_Analysis_and_Gene_Mapping_couv-sofedis.jpg 17 14 20240913T181941+0200 01 P15 EDP Sciences & Science Press 01 01 P15 EDP Sciences & Science Press 04 11 00 20230707 01 00 20230707 19 00 20230707 2026 06 3052868830012 01 WORLD 13 03 9782759830428 15 9782759830428 WORLD 08 EDP Sciences & 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