Linkage Analysis and Gene Mapping, livre ebook
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532
pages
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English
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Ebooks
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2023
Écrit par
Jiankang WANG
Huihui LI
Luyan ZHANG
Publié par
EDP Sciences
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532
pages
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English
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Ebooks
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2023
Description
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.
Preface..................................................... III CHAPTER 1 Populations in Genetic Studies................................... 1 1.1 Commonly Used Populations in Genetic Studies ................. 2 1.1.1 Bi-Parental Populations.............................. 2 1.1.2 Multi-Parental Populations........................... 5 1.1.3 Considerations in Developing Genetic Populations .......... 9 1.2 Preliminary Analysis of Genotypic Data....................... 12 1.2.1 Collection and Coding of Genotypic Data................ 12 1.2.2 Gene Frequency and Genotypic Frequency................ 17 1.2.3 Fitness Test on Genotypic Frequencies................... 18 1.3 Genetic Effect and Genetic Variance.......................... 20 1.3.1 Calculation of Population Mean and Phenotypic Variance .... 20 1.3.2 One-Locus Additive and Dominance Model............... 23 1.3.3 Population Mean and Genetic Variance at One Locus ....... 24 1.4 ANOVA on Single Environment Trials........................ 27 1.4.1 Linear Decomposition on Phenotypic Observation .......... 27 1.4.2 Decomposition of Sum of Squares of Phenotypic Deviations ... 28 1.4.3 Single Environmental ANOVA on Rice Grain Length ........ 31 1.5 ANOVA on Multi-Environment Trials......................... 32 1.5.1 Linear Decomposition on Phenotypic Observation .......... 32 1.5.2 Decomposition 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 from Single Environmental Trials....................... 39 1.6.2 Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials....................... 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 Generation Transition Matrix............................... 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 Transition Matrix of Doubled Haploid................... 58 2.1.5 Transition Matrix of Repeated Selfing................... 59 2.1.6 Expression of the Two-Locus Genotypic Frequencies in Matrix Format................................... 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 2.2.3 Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations ............................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-DominantLocus and One Recessive Locus in TemporaryPopulations................ 69 2.2.6 Genotypic Frequencies of Two DominantLoci in Temporary Populations....................................... 74 2.2.7 Genotypic Frequencies of One DominantLocus and One Recessive Locus in Temporary Populations................ 74 2.2.8 Genotypic Frequencies of Two Recessive Loci in Temporary Populations....................................... 77 2.3 Estimation of Two-Point Recombination Frequency .............. 77 2.3.1 Maximum Likelihood Estimation of Recombination Frequency in DH Populations.......................... 77 2.3.2 General Procedure on the Maximum Likelihood Estimation of Recombination Frequency.......................... 81 2.3.3 Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 population.... 86 2.3.4 Initial Values in Newton Algorithm..................... 87 2.3.5 EM Algorithm in Estimating Recombination Frequency in F2 Populations .......................................90 2.3.6 Effects on the Estimation of Recombination Frequency from Segregation Distortion............................... 92 Exercises................................................... 95 CHAPTER 3 Three-Point Analysis and Linkage Map Construction.................. 101 3.1 Three-Point Analysis and MappingFunction.................... 102 3.1.1 Genetic Interference and Coefficient ofInterference ......... 102 3.1.2 Mapping Function.................................. 105 3.2 Construction of Genetic Linkage Maps........................ 107 3.2.1 Marker Grouping Algorithm........................... 107 3.2.2 Marker Ordering Algorithm........................... 111 3.2.3 Use of the k-Optimal Algorithm in Linkage Map Construction . 113 3.2.4 Rippling of the Ordered Markers....................... 117 3.2.5 Integration of Multiple Maps.......................... 118 3.3 Comparison of the Recombination FrequencyEstimation in Different Populations.............................................121 3.3.1 LOD Score in Testing the LinkageRelationship in Different Populations....................................... 121 3.3.2 Accuracy of the Estimated Recombination Frequency ........ 123 3.3.3 Least Population Size to Declare the Significant Linkage Relationship and Close Linkage........................ 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 to Haploid Gametes................................. 130 3.4.3 Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating.................. 132 Exercises................................................... 134 CHAPTER 4 Single Marker Analysis and Simple IntervalMapping .................. 139 4.1 Single Marker Analysis.................................... 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 Problems with Single Marker Analysis................... 153 4.2 Simple Interval Mapping................................... 154 4.2.1 Frequencies of the QTL Genotypes in a Marker Interval ...... 154 4.2.2 Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes.................................. 161 4.2.3 Testing for the Existence of QTL....................... 166 4.2.4 Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance.............................. 167 4.2.5 Applications of Simple Interval Mapping in DH and F2 Populations....................................... 168 4.2.6 Phenomenon of ‘Ghost’ QTL in SimpleInterval Mapping .... 171 4.2.7 Other Problems with Simple Interval Mapping ............. 172 4.3 Threshold Values of LOD Score in QTL Mapping ................ 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 in the Absence of Any QTL........................... 176 4.3.3 Factors Affecting the Distribution of the Genome-Wide Largest LOD Score................................. 177 4.3.4 Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping.......................... 180 4.3.5 Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping................................... 184 Exercises................................................... 189 CHAPTER 5 Inclusive Composite Interval Mapping............................. 195 5.1 Importance of the Control on Background Genetic Variation in QTL Mapping............................................... 196 5.2 Inclusive Composite Interval Mapping in DH Populations .......... 199 5.2.1 Additive Genetic Model of One Single QTL............... 199 5.2.2 Additive Genetic Model for Multiple QTLs............... 201 5.2.3 One-Dimensional Scanning and HypothesisTesting for Additive QTLs.................................. 202 5.2.4 Application of ICIM in a DH Mapping Population in Barley . . 204 5.3 Inclusive Composite Interval Mapping in F2 Populations ........... 208 5.3.1 Additive and Dominant Model of One Single QTL .......... 208 5.3.2 Additive and Dominant Model for Multiple QTLs .......... 212 5.3.3 One-Dimensional Scanning and HypothesisTesting in Additive and Dominant QTL Mapping................ 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 QTL Detection.............................................. 216 5.4.1 Type II Error and Statistical Power inHypothesis Testing .... 216 5.4.2 Probability of Two Types of Error and the Appropriate Sample Size....................................... 220 5.4.3 Distribution and Effect Models of QTLs Used in Power Analysis by Simulations.............................. 222 5.4.4 Calculation of the Detection Power and False Discovery Rate in QTL Mapping ...................................224 5.5 Comparison of IM and ICIM by Simulation.................... 230 5.5.1 QTL Detection Power and FDR from IM................. 230 5.5.2 QTL Detection Power and FDR from ICIM............... 232