Linkage Analysis and Gene Mapping.:
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 t...
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| Format: | Elektronisch E-Book |
| Sprache: | English |
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Les Ulis :
EDP Sciences,
2023.
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| Ausgabe: | 1st ed. |
| Schriftenreihe: | Current Natural Sciences Series.
|
| Schlagworte: | |
| Online-Zugang: | DE-862 DE-863 |
| Zusammenfassung: | 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. |
| Beschreibung: | Inclusive Composite Interval Mapping (ICIM) in the Double Cross F1 Population. |
| Beschreibung: | 1 online resource (532 pages). |
| ISBN: | 2759830438 9782759830435 |
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| 100 | 1 | |a WANG, Jiankang. | |
| 245 | 1 | 0 | |a Linkage Analysis and Gene Mapping. |
| 250 | |a 1st ed. | ||
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| 264 | 4 | |c ©2023. | |
| 300 | |a 1 online resource (532 pages). | ||
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| 490 | 1 | |a Current Natural Sciences Series | |
| 505 | 0 | |a Intro -- Linkage Analysis and Gene Mapping -- Preface -- Contents -- Populations in Genetic Studies -- Commonly Used Populations in Genetic Studies -- Bi-Parental Populations -- Multi-Parental Populations -- Considerations in Developing Genetic Populations -- Preliminary Analysis of Genotypic Data -- Collection and Coding of Genotypic Data -- Gene Frequency and Genotypic Frequency -- Fitness Test on Genotypic Frequencies -- Genetic Effect and Genetic Variance -- Calculation of Population Mean and Phenotypic Variance -- One-Locus Additive and Dominance Model -- Population Mean and Genetic Variance at One Locus -- ANOVA on Single Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Single Environmental ANOVA on Rice Grain Length -- ANOVA on Multi-Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Multi-Environmental ANOVA on Rice Grain Length -- Estimation of Genotypic Values and the Broad-Sense Heritability -- Genotypic Values and Broad-Sense Heritability from Single Environmental Trials -- Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials -- Estimation of Genotypic Values Under Heterogeneous Error Variances -- Exercises -- Estimation of the Two-Point Recombination Frequencies -- Generation Transition Matrix -- Usefulness of the Transition Matrix in Linkage Analysis -- Transition Matrix of One Generation of Backcrossing -- Transition Matrix of One Generation of Selfing -- Transition Matrix of Doubled Haploid -- Transition Matrix of Repeated Selfing -- Expression of the Two-Locus Genotypic Frequencies in Matrix Format -- Theoretical Genotypic Frequencies at Two Loci -- Theoretical Frequencies of 10 Genotypes at Two Loci. | |
| 505 | 8 | |a Theoretical Frequencies of 4 Homozygotes in Permanent Populations -- Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Recessive Loci in Temporary Populations -- Estimation of Two-Point Recombination Frequency -- Maximum Likelihood Estimation of Recombination Frequency in DH Populations -- General Procedure on the Maximum Likelihood Estimation of Recombination Frequency -- Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 Population -- Initial Values in Newton Algorithm -- EM Algorithm in Estimating Recombination Frequency in F2 Populations -- Effects on the Estimation of Recombination Frequency from Segregation Distortion -- Exercises -- Three-Point Analysis and Linkage Map Construction -- Three-Point Analysis and Mapping Function -- Genetic Interference and Coefficient of Interference -- Mapping Function -- Construction of Genetic Linkage Maps -- Marker Grouping Algorithm -- Marker Ordering Algorithm -- Use of the k-Optimal Algorithm in Linkage Map Construction -- Rippling of the Ordered Markers -- Integration of Multiple Maps -- Comparison of the Recombination Frequency Estimation in Different Populations -- LOD Score in Testing the Linkage Relationship in Different Populations -- Accuracy of the Estimated Recombination Frequency -- Least Population Size to Declare the Significant Linkage Relationship and Close Linkage -- Linkage Analysis in Random Mating Populations. | |
| 505 | 8 | |a Linkage Dis-Equilibrium in Random Mating Populations -- Generation Transition Matrix from Diploid Genotypes to Haploid Gametes -- Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating -- Exercises -- Single Marker Analysis and Simple Interval Mapping -- Single Marker Analysis -- Phenotypic Means of Different Genotypes at One Marker Locus -- Single Marker Analysis by t-Test in Populations with Two Genotypes -- Single Marker Analysis by t-Test in Populations with Three Genotypes -- ANOVA in Single Marker Analysis in Populations with Three Genotypes -- Likelihood Ratio Test in Single Marker Analysis -- Problems with Single Marker Analysis -- Simple Interval Mapping -- Frequencies of the QTL Genotypes in a Marker Interval -- Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes -- Testing for the Existence of QTL -- Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance -- Applications of Simple Interval Mapping in DH and F2 Populations -- Phenomenon of 'Ghost' QTL in Simple Interval Mapping -- Other Problems with Simple Interval Mapping -- Threshold Values of LOD Score in QTL Mapping -- Significance Level and Critical Value of One Test Statistic -- Distribution of the LRT Statistic at Single Scanning Positions in the Absence of Any QTL -- Factors Affecting the Distribution of the Genome-Wide Largest LOD Score -- Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping -- Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping -- Exercises -- Inclusive Composite Interval Mapping -- Importance of the Control on Background Genetic Variation in QTL Mapping -- Inclusive Composite Interval Mapping in DH Populations -- Additive Genetic Model of One Single QTL -- Additive Genetic Model for Multiple QTLs. | |
| 505 | 8 | |a One-Dimensional Scanning and Hypothesis Testing for Additive QTLs -- Application of ICIM in a DH Mapping Population in Barley -- Inclusive Composite Interval Mapping in F2 Populations -- Additive and Dominant Model of One Single QTL -- Additive and Dominant Model for Multiple QTLs -- One-Dimensional Scanning and Hypothesis Testing in Additive and Dominant QTL Mapping -- Application of ICIM in an F2 Mapping Population -- Type II Error in Hypothesis Testing and Statistical Power in QTL Detection -- Type II Error and Statistical Power in Hypothesis Testing -- Probability of Two Types of Error and the Appropriate Sample Size -- Distribution and Effect Models of QTLs Used in Power Analysis by Simulations -- Calculation of the Detection Power and False Discovery Rate in QTL Mapping -- Comparison of IM and ICIM by Simulation -- QTL Detection Power and FDR from IM -- QTL Detection Power and FDR from ICIM -- Detection Powers Counted by Marker Intervals -- Suitable Population Size Required in QTL Mapping -- Avoiding the Overfitting Problem in the First Step of Model Selection in ICIM -- Exercises -- QTL Mapping for Epistasis and Genotype-by-Environment Interaction -- Epistatic QTL Mapping in DH Populations -- Linear Regression in Epistatic QTL Mapping and the Statistical Properties -- Two-Dimensional Scanning on Di-Genic Epistatic QTLs -- Genetic Variance on Epistatic QTLs with Linkage -- Simulation Study on Epistatic QTL Mapping in DH Populations -- Epistatic QTL Mapping in F2 Populations -- The Di-Genic Epistasis Model in F2 Populations -- Epistatic QTL Mapping Procedure in F2 Population -- Detection Power of Epistatic QTLs in F2 Populations -- Genetic Analysis and Detection Power of the Most Common Di-Genic Interactions -- Genetic Effects in Di-Genic Interactions -- Decomposition of Genetic Variance at the Presence of Di-Genic Epistasis. | |
| 505 | 8 | |a Power Simulation of Epistatic QTL Mapping -- Issues in Epistatic QTL Mapping -- Mapping of the QTL by Environment Interactions -- Mapping of the Additive QTL by Environment Interactions -- Mapping of the Epistatic QTL and Environment Interactions -- QTL and Environment Interactions in One Actual RIL Population in Maize -- Exercises -- Genetic Analysis in Hybrid F1 of Two Heterozygous Parents and Double-Cross F1 of Four Homozygous Parents -- Linage Analysis in the Hybrid F1 Derived from Two Heterozygous Parents -- Categories of Polymorphism Markers -- Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci -- Estimation of the Recombination Frequency Between Two Fully-Informative Markers -- Haploid Type Rebuilding in the Heterozygous Parents -- Estimation of the Recombination Frequency for Incompletely Informative Markers -- Theoretical Frequencies of Identifiable Genotypes Between the Complete Marker and Other Three Categories of Markers -- Theoretical Frequencies of Identifiable Genotypes Between Two Markers Belonging to Category II, III, or IV -- Theoretical Frequencies of Identifiable Genotypes Between Two Category IV Markers -- Haploid Type Rebuilding at the Presence of All Categories of Markers -- Linkage Analysis in Double Cross F1 Derived from Four Pure-Line Parents -- Marker Categories and Estimation of Recombination Frequency in the Double Cross F1 Population -- Equivalence Between the Double Cross F1 of Pure-Line Parents and Hybrid F1 of Heterozygous Parents -- Genotypic Frequencies at Three Complete Markers -- Imputation of Incomplete and Missing Marker Information -- QTL Mapping in the Double Cross F1 Population Derived from Four Pure-Line Parents -- One-QTL Genetic Model in Double Cross F1 Population -- The Linear Regression Model of the Phenotype on Marker Type for Multiple QTLs. | |
| 500 | |a Inclusive Composite Interval Mapping (ICIM) in the Double Cross F1 Population. | ||
| 520 | |a 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. | ||
| 588 | |a Description based on publisher supplied metadata and other sources. | ||
| 650 | 0 | |a Genomics |x Mathematics. | |
| 650 | 6 | |a Génomique |x Mathématiques. | |
| 650 | 7 | |a SCIENCE / Life Sciences / Genetics & Genomics. |2 bisacsh | |
| 700 | 1 | |a LI, Huihui. | |
| 700 | 1 | |a ZHANG, Luyan. | |
| 776 | 0 | 8 | |i Print version: |z 9782759830428 |
| 830 | 0 | |a Current Natural Sciences Series. | |
| 966 | 4 | 0 | |l DE-862 |p ZDB-4-EBA |q FWS_PDA_EBA |u https://search.ebscohost.com/login.aspx?direct=true&scope=site&db=nlebk&AN=3628877 |3 Volltext |
| 966 | 4 | 0 | |l DE-863 |p ZDB-4-EBA |q FWS_PDA_EBA |u https://search.ebscohost.com/login.aspx?direct=true&scope=site&db=nlebk&AN=3628877 |3 Volltext |
| 938 | |a De Gruyter |b DEGR |n 9782759830435 | ||
| 938 | |a ProQuest Ebook Central |b EBLB |n EBL30800067 | ||
| 938 | |a EBSCOhost |b EBSC |n 3628877 | ||
| 994 | |a 92 |b GEBAY | ||
| 912 | |a ZDB-4-EBA | ||
| 049 | |a DE-862 | ||
| 049 | |a DE-863 | ||
Datensatz im Suchindex
| DE-BY-FWS_katkey | ZDB-4-EBA-on1396937748 |
|---|---|
| _version_ | 1829095381417328641 |
| adam_text | |
| any_adam_object | |
| author | WANG, Jiankang |
| author2 | LI, Huihui ZHANG, Luyan |
| author2_role | |
| author2_variant | h l hl l z lz |
| author_facet | WANG, Jiankang LI, Huihui ZHANG, Luyan |
| author_role | |
| author_sort | WANG, Jiankang |
| author_variant | j w jw |
| building | Verbundindex |
| bvnumber | localFWS |
| callnumber-first | Q - Science |
| callnumber-label | QH447 |
| callnumber-raw | QH447 |
| callnumber-search | QH447 |
| callnumber-sort | QH 3447 |
| callnumber-subject | QH - Natural History and Biology |
| collection | ZDB-4-EBA |
| contents | Intro -- Linkage Analysis and Gene Mapping -- Preface -- Contents -- Populations in Genetic Studies -- Commonly Used Populations in Genetic Studies -- Bi-Parental Populations -- Multi-Parental Populations -- Considerations in Developing Genetic Populations -- Preliminary Analysis of Genotypic Data -- Collection and Coding of Genotypic Data -- Gene Frequency and Genotypic Frequency -- Fitness Test on Genotypic Frequencies -- Genetic Effect and Genetic Variance -- Calculation of Population Mean and Phenotypic Variance -- One-Locus Additive and Dominance Model -- Population Mean and Genetic Variance at One Locus -- ANOVA on Single Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Single Environmental ANOVA on Rice Grain Length -- ANOVA on Multi-Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Multi-Environmental ANOVA on Rice Grain Length -- Estimation of Genotypic Values and the Broad-Sense Heritability -- Genotypic Values and Broad-Sense Heritability from Single Environmental Trials -- Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials -- Estimation of Genotypic Values Under Heterogeneous Error Variances -- Exercises -- Estimation of the Two-Point Recombination Frequencies -- Generation Transition Matrix -- Usefulness of the Transition Matrix in Linkage Analysis -- Transition Matrix of One Generation of Backcrossing -- Transition Matrix of One Generation of Selfing -- Transition Matrix of Doubled Haploid -- Transition Matrix of Repeated Selfing -- Expression of the Two-Locus Genotypic Frequencies in Matrix Format -- Theoretical Genotypic Frequencies at Two Loci -- Theoretical Frequencies of 10 Genotypes at Two Loci. Theoretical Frequencies of 4 Homozygotes in Permanent Populations -- Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Recessive Loci in Temporary Populations -- Estimation of Two-Point Recombination Frequency -- Maximum Likelihood Estimation of Recombination Frequency in DH Populations -- General Procedure on the Maximum Likelihood Estimation of Recombination Frequency -- Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 Population -- Initial Values in Newton Algorithm -- EM Algorithm in Estimating Recombination Frequency in F2 Populations -- Effects on the Estimation of Recombination Frequency from Segregation Distortion -- Exercises -- Three-Point Analysis and Linkage Map Construction -- Three-Point Analysis and Mapping Function -- Genetic Interference and Coefficient of Interference -- Mapping Function -- Construction of Genetic Linkage Maps -- Marker Grouping Algorithm -- Marker Ordering Algorithm -- Use of the k-Optimal Algorithm in Linkage Map Construction -- Rippling of the Ordered Markers -- Integration of Multiple Maps -- Comparison of the Recombination Frequency Estimation in Different Populations -- LOD Score in Testing the Linkage Relationship in Different Populations -- Accuracy of the Estimated Recombination Frequency -- Least Population Size to Declare the Significant Linkage Relationship and Close Linkage -- Linkage Analysis in Random Mating Populations. Linkage Dis-Equilibrium in Random Mating Populations -- Generation Transition Matrix from Diploid Genotypes to Haploid Gametes -- Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating -- Exercises -- Single Marker Analysis and Simple Interval Mapping -- Single Marker Analysis -- Phenotypic Means of Different Genotypes at One Marker Locus -- Single Marker Analysis by t-Test in Populations with Two Genotypes -- Single Marker Analysis by t-Test in Populations with Three Genotypes -- ANOVA in Single Marker Analysis in Populations with Three Genotypes -- Likelihood Ratio Test in Single Marker Analysis -- Problems with Single Marker Analysis -- Simple Interval Mapping -- Frequencies of the QTL Genotypes in a Marker Interval -- Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes -- Testing for the Existence of QTL -- Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance -- Applications of Simple Interval Mapping in DH and F2 Populations -- Phenomenon of 'Ghost' QTL in Simple Interval Mapping -- Other Problems with Simple Interval Mapping -- Threshold Values of LOD Score in QTL Mapping -- Significance Level and Critical Value of One Test Statistic -- Distribution of the LRT Statistic at Single Scanning Positions in the Absence of Any QTL -- Factors Affecting the Distribution of the Genome-Wide Largest LOD Score -- Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping -- Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping -- Exercises -- Inclusive Composite Interval Mapping -- Importance of the Control on Background Genetic Variation in QTL Mapping -- Inclusive Composite Interval Mapping in DH Populations -- Additive Genetic Model of One Single QTL -- Additive Genetic Model for Multiple QTLs. One-Dimensional Scanning and Hypothesis Testing for Additive QTLs -- Application of ICIM in a DH Mapping Population in Barley -- Inclusive Composite Interval Mapping in F2 Populations -- Additive and Dominant Model of One Single QTL -- Additive and Dominant Model for Multiple QTLs -- One-Dimensional Scanning and Hypothesis Testing in Additive and Dominant QTL Mapping -- Application of ICIM in an F2 Mapping Population -- Type II Error in Hypothesis Testing and Statistical Power in QTL Detection -- Type II Error and Statistical Power in Hypothesis Testing -- Probability of Two Types of Error and the Appropriate Sample Size -- Distribution and Effect Models of QTLs Used in Power Analysis by Simulations -- Calculation of the Detection Power and False Discovery Rate in QTL Mapping -- Comparison of IM and ICIM by Simulation -- QTL Detection Power and FDR from IM -- QTL Detection Power and FDR from ICIM -- Detection Powers Counted by Marker Intervals -- Suitable Population Size Required in QTL Mapping -- Avoiding the Overfitting Problem in the First Step of Model Selection in ICIM -- Exercises -- QTL Mapping for Epistasis and Genotype-by-Environment Interaction -- Epistatic QTL Mapping in DH Populations -- Linear Regression in Epistatic QTL Mapping and the Statistical Properties -- Two-Dimensional Scanning on Di-Genic Epistatic QTLs -- Genetic Variance on Epistatic QTLs with Linkage -- Simulation Study on Epistatic QTL Mapping in DH Populations -- Epistatic QTL Mapping in F2 Populations -- The Di-Genic Epistasis Model in F2 Populations -- Epistatic QTL Mapping Procedure in F2 Population -- Detection Power of Epistatic QTLs in F2 Populations -- Genetic Analysis and Detection Power of the Most Common Di-Genic Interactions -- Genetic Effects in Di-Genic Interactions -- Decomposition of Genetic Variance at the Presence of Di-Genic Epistasis. Power Simulation of Epistatic QTL Mapping -- Issues in Epistatic QTL Mapping -- Mapping of the QTL by Environment Interactions -- Mapping of the Additive QTL by Environment Interactions -- Mapping of the Epistatic QTL and Environment Interactions -- QTL and Environment Interactions in One Actual RIL Population in Maize -- Exercises -- Genetic Analysis in Hybrid F1 of Two Heterozygous Parents and Double-Cross F1 of Four Homozygous Parents -- Linage Analysis in the Hybrid F1 Derived from Two Heterozygous Parents -- Categories of Polymorphism Markers -- Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci -- Estimation of the Recombination Frequency Between Two Fully-Informative Markers -- Haploid Type Rebuilding in the Heterozygous Parents -- Estimation of the Recombination Frequency for Incompletely Informative Markers -- Theoretical Frequencies of Identifiable Genotypes Between the Complete Marker and Other Three Categories of Markers -- Theoretical Frequencies of Identifiable Genotypes Between Two Markers Belonging to Category II, III, or IV -- Theoretical Frequencies of Identifiable Genotypes Between Two Category IV Markers -- Haploid Type Rebuilding at the Presence of All Categories of Markers -- Linkage Analysis in Double Cross F1 Derived from Four Pure-Line Parents -- Marker Categories and Estimation of Recombination Frequency in the Double Cross F1 Population -- Equivalence Between the Double Cross F1 of Pure-Line Parents and Hybrid F1 of Heterozygous Parents -- Genotypic Frequencies at Three Complete Markers -- Imputation of Incomplete and Missing Marker Information -- QTL Mapping in the Double Cross F1 Population Derived from Four Pure-Line Parents -- One-QTL Genetic Model in Double Cross F1 Population -- The Linear Regression Model of the Phenotype on Marker Type for Multiple QTLs. |
| ctrlnum | (OCoLC)1396937748 |
| dewey-full | 572.86 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.86 |
| dewey-search | 572.86 |
| dewey-sort | 3572.86 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| edition | 1st ed. |
| format | Electronic eBook |
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code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">computer</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">online resource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="490" ind1="1" ind2=" "><subfield code="a">Current Natural Sciences Series</subfield></datafield><datafield tag="505" ind1="0" ind2=" "><subfield code="a">Intro -- Linkage Analysis and Gene Mapping -- Preface -- Contents -- Populations in Genetic Studies -- Commonly Used Populations in Genetic Studies -- Bi-Parental Populations -- Multi-Parental Populations -- Considerations in Developing Genetic Populations -- Preliminary Analysis of Genotypic Data -- Collection and Coding of Genotypic Data -- Gene Frequency and Genotypic Frequency -- Fitness Test on Genotypic Frequencies -- Genetic Effect and Genetic Variance -- Calculation of Population Mean and Phenotypic Variance -- One-Locus Additive and Dominance Model -- Population Mean and Genetic Variance at One Locus -- ANOVA on Single Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Single Environmental ANOVA on Rice Grain Length -- ANOVA on Multi-Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Multi-Environmental ANOVA on Rice Grain Length -- Estimation of Genotypic Values and the Broad-Sense Heritability -- Genotypic Values and Broad-Sense Heritability from Single Environmental Trials -- Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials -- Estimation of Genotypic Values Under Heterogeneous Error Variances -- Exercises -- Estimation of the Two-Point Recombination Frequencies -- Generation Transition Matrix -- Usefulness of the Transition Matrix in Linkage Analysis -- Transition Matrix of One Generation of Backcrossing -- Transition Matrix of One Generation of Selfing -- Transition Matrix of Doubled Haploid -- Transition Matrix of Repeated Selfing -- Expression of the Two-Locus Genotypic Frequencies in Matrix Format -- Theoretical Genotypic Frequencies at Two Loci -- Theoretical Frequencies of 10 Genotypes at Two Loci.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">Theoretical Frequencies of 4 Homozygotes in Permanent Populations -- Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Recessive Loci in Temporary Populations -- Estimation of Two-Point Recombination Frequency -- Maximum Likelihood Estimation of Recombination Frequency in DH Populations -- General Procedure on the Maximum Likelihood Estimation of Recombination Frequency -- Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 Population -- Initial Values in Newton Algorithm -- EM Algorithm in Estimating Recombination Frequency in F2 Populations -- Effects on the Estimation of Recombination Frequency from Segregation Distortion -- Exercises -- Three-Point Analysis and Linkage Map Construction -- Three-Point Analysis and Mapping Function -- Genetic Interference and Coefficient of Interference -- Mapping Function -- Construction of Genetic Linkage Maps -- Marker Grouping Algorithm -- Marker Ordering Algorithm -- Use of the k-Optimal Algorithm in Linkage Map Construction -- Rippling of the Ordered Markers -- Integration of Multiple Maps -- Comparison of the Recombination Frequency Estimation in Different Populations -- LOD Score in Testing the Linkage Relationship in Different Populations -- Accuracy of the Estimated Recombination Frequency -- Least Population Size to Declare the Significant Linkage Relationship and Close Linkage -- Linkage Analysis in Random Mating Populations.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">Linkage Dis-Equilibrium in Random Mating Populations -- Generation Transition Matrix from Diploid Genotypes to Haploid Gametes -- Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating -- Exercises -- Single Marker Analysis and Simple Interval Mapping -- Single Marker Analysis -- Phenotypic Means of Different Genotypes at One Marker Locus -- Single Marker Analysis by t-Test in Populations with Two Genotypes -- Single Marker Analysis by t-Test in Populations with Three Genotypes -- ANOVA in Single Marker Analysis in Populations with Three Genotypes -- Likelihood Ratio Test in Single Marker Analysis -- Problems with Single Marker Analysis -- Simple Interval Mapping -- Frequencies of the QTL Genotypes in a Marker Interval -- Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes -- Testing for the Existence of QTL -- Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance -- Applications of Simple Interval Mapping in DH and F2 Populations -- Phenomenon of 'Ghost' QTL in Simple Interval Mapping -- Other Problems with Simple Interval Mapping -- Threshold Values of LOD Score in QTL Mapping -- Significance Level and Critical Value of One Test Statistic -- Distribution of the LRT Statistic at Single Scanning Positions in the Absence of Any QTL -- Factors Affecting the Distribution of the Genome-Wide Largest LOD Score -- Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping -- Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping -- Exercises -- Inclusive Composite Interval Mapping -- Importance of the Control on Background Genetic Variation in QTL Mapping -- Inclusive Composite Interval Mapping in DH Populations -- Additive Genetic Model of One Single QTL -- Additive Genetic Model for Multiple QTLs.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">One-Dimensional Scanning and Hypothesis Testing for Additive QTLs -- Application of ICIM in a DH Mapping Population in Barley -- Inclusive Composite Interval Mapping in F2 Populations -- Additive and Dominant Model of One Single QTL -- Additive and Dominant Model for Multiple QTLs -- One-Dimensional Scanning and Hypothesis Testing in Additive and Dominant QTL Mapping -- Application of ICIM in an F2 Mapping Population -- Type II Error in Hypothesis Testing and Statistical Power in QTL Detection -- Type II Error and Statistical Power in Hypothesis Testing -- Probability of Two Types of Error and the Appropriate Sample Size -- Distribution and Effect Models of QTLs Used in Power Analysis by Simulations -- Calculation of the Detection Power and False Discovery Rate in QTL Mapping -- Comparison of IM and ICIM by Simulation -- QTL Detection Power and FDR from IM -- QTL Detection Power and FDR from ICIM -- Detection Powers Counted by Marker Intervals -- Suitable Population Size Required in QTL Mapping -- Avoiding the Overfitting Problem in the First Step of Model Selection in ICIM -- Exercises -- QTL Mapping for Epistasis and Genotype-by-Environment Interaction -- Epistatic QTL Mapping in DH Populations -- Linear Regression in Epistatic QTL Mapping and the Statistical Properties -- Two-Dimensional Scanning on Di-Genic Epistatic QTLs -- Genetic Variance on Epistatic QTLs with Linkage -- Simulation Study on Epistatic QTL Mapping in DH Populations -- Epistatic QTL Mapping in F2 Populations -- The Di-Genic Epistasis Model in F2 Populations -- Epistatic QTL Mapping Procedure in F2 Population -- Detection Power of Epistatic QTLs in F2 Populations -- Genetic Analysis and Detection Power of the Most Common Di-Genic Interactions -- Genetic Effects in Di-Genic Interactions -- Decomposition of Genetic Variance at the Presence of Di-Genic Epistasis.</subfield></datafield><datafield tag="505" ind1="8" ind2=" "><subfield code="a">Power Simulation of Epistatic QTL Mapping -- Issues in Epistatic QTL Mapping -- Mapping of the QTL by Environment Interactions -- Mapping of the Additive QTL by Environment Interactions -- Mapping of the Epistatic QTL and Environment Interactions -- QTL and Environment Interactions in One Actual RIL Population in Maize -- Exercises -- Genetic Analysis in Hybrid F1 of Two Heterozygous Parents and Double-Cross F1 of Four Homozygous Parents -- Linage Analysis in the Hybrid F1 Derived from Two Heterozygous Parents -- Categories of Polymorphism Markers -- Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci -- Estimation of the Recombination Frequency Between Two Fully-Informative Markers -- Haploid Type Rebuilding in the Heterozygous Parents -- Estimation of the Recombination Frequency for Incompletely Informative Markers -- Theoretical Frequencies of Identifiable Genotypes Between the Complete Marker and Other Three Categories of Markers -- Theoretical Frequencies of Identifiable Genotypes Between Two Markers Belonging to Category II, III, or IV -- Theoretical Frequencies of Identifiable Genotypes Between Two Category IV Markers -- Haploid Type Rebuilding at the Presence of All Categories of Markers -- Linkage Analysis in Double Cross F1 Derived from Four Pure-Line Parents -- Marker Categories and Estimation of Recombination Frequency in the Double Cross F1 Population -- Equivalence Between the Double Cross F1 of Pure-Line Parents and Hybrid F1 of Heterozygous Parents -- Genotypic Frequencies at Three Complete Markers -- Imputation of Incomplete and Missing Marker Information -- QTL Mapping in the Double Cross F1 Population Derived from Four Pure-Line Parents -- One-QTL Genetic Model in Double Cross F1 Population -- The Linear Regression Model of the Phenotype on Marker Type for Multiple QTLs.</subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a">Inclusive Composite Interval Mapping (ICIM) in the Double Cross F1 Population.</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">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.</subfield></datafield><datafield tag="588" ind1=" " ind2=" "><subfield code="a">Description based on publisher supplied metadata and other sources.</subfield></datafield><datafield tag="650" ind1=" " ind2="0"><subfield code="a">Genomics</subfield><subfield code="x">Mathematics.</subfield></datafield><datafield tag="650" ind1=" " ind2="6"><subfield code="a">Génomique</subfield><subfield code="x">Mathématiques.</subfield></datafield><datafield tag="650" ind1=" " ind2="7"><subfield code="a">SCIENCE / Life Sciences / Genetics & Genomics.</subfield><subfield code="2">bisacsh</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">LI, Huihui.</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">ZHANG, Luyan.</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Print version:</subfield><subfield code="z">9782759830428</subfield></datafield><datafield tag="830" ind1=" " ind2="0"><subfield code="a">Current Natural Sciences Series.</subfield></datafield><datafield tag="966" ind1="4" ind2="0"><subfield code="l">DE-862</subfield><subfield code="p">ZDB-4-EBA</subfield><subfield code="q">FWS_PDA_EBA</subfield><subfield code="u">https://search.ebscohost.com/login.aspx?direct=true&scope=site&db=nlebk&AN=3628877</subfield><subfield code="3">Volltext</subfield></datafield><datafield tag="966" ind1="4" ind2="0"><subfield code="l">DE-863</subfield><subfield code="p">ZDB-4-EBA</subfield><subfield code="q">FWS_PDA_EBA</subfield><subfield code="u">https://search.ebscohost.com/login.aspx?direct=true&scope=site&db=nlebk&AN=3628877</subfield><subfield code="3">Volltext</subfield></datafield><datafield tag="938" ind1=" " ind2=" "><subfield code="a">De Gruyter</subfield><subfield code="b">DEGR</subfield><subfield code="n">9782759830435</subfield></datafield><datafield tag="938" ind1=" " ind2=" "><subfield code="a">ProQuest Ebook Central</subfield><subfield code="b">EBLB</subfield><subfield code="n">EBL30800067</subfield></datafield><datafield tag="938" ind1=" " ind2=" "><subfield code="a">EBSCOhost</subfield><subfield code="b">EBSC</subfield><subfield code="n">3628877</subfield></datafield><datafield tag="994" ind1=" " ind2=" "><subfield code="a">92</subfield><subfield code="b">GEBAY</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">ZDB-4-EBA</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-862</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-863</subfield></datafield></record></collection> |
| id | ZDB-4-EBA-on1396937748 |
| illustrated | Not Illustrated |
| indexdate | 2025-04-11T08:48:07Z |
| institution | BVB |
| isbn | 2759830438 9782759830435 |
| language | English |
| oclc_num | 1396937748 |
| open_access_boolean | |
| owner | MAIN DE-862 DE-BY-FWS DE-863 DE-BY-FWS |
| owner_facet | MAIN DE-862 DE-BY-FWS DE-863 DE-BY-FWS |
| physical | 1 online resource (532 pages). |
| psigel | ZDB-4-EBA FWS_PDA_EBA ZDB-4-EBA |
| publishDate | 2023 |
| publishDateSearch | 2023 |
| publishDateSort | 2023 |
| publisher | EDP Sciences, |
| record_format | marc |
| series | Current Natural Sciences Series. |
| series2 | Current Natural Sciences Series |
| spelling | WANG, Jiankang. Linkage Analysis and Gene Mapping. 1st ed. Les Ulis : EDP Sciences, 2023. ©2023. 1 online resource (532 pages). text txt rdacontent computer c rdamedia online resource cr rdacarrier Current Natural Sciences Series Intro -- Linkage Analysis and Gene Mapping -- Preface -- Contents -- Populations in Genetic Studies -- Commonly Used Populations in Genetic Studies -- Bi-Parental Populations -- Multi-Parental Populations -- Considerations in Developing Genetic Populations -- Preliminary Analysis of Genotypic Data -- Collection and Coding of Genotypic Data -- Gene Frequency and Genotypic Frequency -- Fitness Test on Genotypic Frequencies -- Genetic Effect and Genetic Variance -- Calculation of Population Mean and Phenotypic Variance -- One-Locus Additive and Dominance Model -- Population Mean and Genetic Variance at One Locus -- ANOVA on Single Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Single Environmental ANOVA on Rice Grain Length -- ANOVA on Multi-Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Multi-Environmental ANOVA on Rice Grain Length -- Estimation of Genotypic Values and the Broad-Sense Heritability -- Genotypic Values and Broad-Sense Heritability from Single Environmental Trials -- Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials -- Estimation of Genotypic Values Under Heterogeneous Error Variances -- Exercises -- Estimation of the Two-Point Recombination Frequencies -- Generation Transition Matrix -- Usefulness of the Transition Matrix in Linkage Analysis -- Transition Matrix of One Generation of Backcrossing -- Transition Matrix of One Generation of Selfing -- Transition Matrix of Doubled Haploid -- Transition Matrix of Repeated Selfing -- Expression of the Two-Locus Genotypic Frequencies in Matrix Format -- Theoretical Genotypic Frequencies at Two Loci -- Theoretical Frequencies of 10 Genotypes at Two Loci. Theoretical Frequencies of 4 Homozygotes in Permanent Populations -- Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Recessive Loci in Temporary Populations -- Estimation of Two-Point Recombination Frequency -- Maximum Likelihood Estimation of Recombination Frequency in DH Populations -- General Procedure on the Maximum Likelihood Estimation of Recombination Frequency -- Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 Population -- Initial Values in Newton Algorithm -- EM Algorithm in Estimating Recombination Frequency in F2 Populations -- Effects on the Estimation of Recombination Frequency from Segregation Distortion -- Exercises -- Three-Point Analysis and Linkage Map Construction -- Three-Point Analysis and Mapping Function -- Genetic Interference and Coefficient of Interference -- Mapping Function -- Construction of Genetic Linkage Maps -- Marker Grouping Algorithm -- Marker Ordering Algorithm -- Use of the k-Optimal Algorithm in Linkage Map Construction -- Rippling of the Ordered Markers -- Integration of Multiple Maps -- Comparison of the Recombination Frequency Estimation in Different Populations -- LOD Score in Testing the Linkage Relationship in Different Populations -- Accuracy of the Estimated Recombination Frequency -- Least Population Size to Declare the Significant Linkage Relationship and Close Linkage -- Linkage Analysis in Random Mating Populations. Linkage Dis-Equilibrium in Random Mating Populations -- Generation Transition Matrix from Diploid Genotypes to Haploid Gametes -- Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating -- Exercises -- Single Marker Analysis and Simple Interval Mapping -- Single Marker Analysis -- Phenotypic Means of Different Genotypes at One Marker Locus -- Single Marker Analysis by t-Test in Populations with Two Genotypes -- Single Marker Analysis by t-Test in Populations with Three Genotypes -- ANOVA in Single Marker Analysis in Populations with Three Genotypes -- Likelihood Ratio Test in Single Marker Analysis -- Problems with Single Marker Analysis -- Simple Interval Mapping -- Frequencies of the QTL Genotypes in a Marker Interval -- Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes -- Testing for the Existence of QTL -- Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance -- Applications of Simple Interval Mapping in DH and F2 Populations -- Phenomenon of 'Ghost' QTL in Simple Interval Mapping -- Other Problems with Simple Interval Mapping -- Threshold Values of LOD Score in QTL Mapping -- Significance Level and Critical Value of One Test Statistic -- Distribution of the LRT Statistic at Single Scanning Positions in the Absence of Any QTL -- Factors Affecting the Distribution of the Genome-Wide Largest LOD Score -- Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping -- Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping -- Exercises -- Inclusive Composite Interval Mapping -- Importance of the Control on Background Genetic Variation in QTL Mapping -- Inclusive Composite Interval Mapping in DH Populations -- Additive Genetic Model of One Single QTL -- Additive Genetic Model for Multiple QTLs. One-Dimensional Scanning and Hypothesis Testing for Additive QTLs -- Application of ICIM in a DH Mapping Population in Barley -- Inclusive Composite Interval Mapping in F2 Populations -- Additive and Dominant Model of One Single QTL -- Additive and Dominant Model for Multiple QTLs -- One-Dimensional Scanning and Hypothesis Testing in Additive and Dominant QTL Mapping -- Application of ICIM in an F2 Mapping Population -- Type II Error in Hypothesis Testing and Statistical Power in QTL Detection -- Type II Error and Statistical Power in Hypothesis Testing -- Probability of Two Types of Error and the Appropriate Sample Size -- Distribution and Effect Models of QTLs Used in Power Analysis by Simulations -- Calculation of the Detection Power and False Discovery Rate in QTL Mapping -- Comparison of IM and ICIM by Simulation -- QTL Detection Power and FDR from IM -- QTL Detection Power and FDR from ICIM -- Detection Powers Counted by Marker Intervals -- Suitable Population Size Required in QTL Mapping -- Avoiding the Overfitting Problem in the First Step of Model Selection in ICIM -- Exercises -- QTL Mapping for Epistasis and Genotype-by-Environment Interaction -- Epistatic QTL Mapping in DH Populations -- Linear Regression in Epistatic QTL Mapping and the Statistical Properties -- Two-Dimensional Scanning on Di-Genic Epistatic QTLs -- Genetic Variance on Epistatic QTLs with Linkage -- Simulation Study on Epistatic QTL Mapping in DH Populations -- Epistatic QTL Mapping in F2 Populations -- The Di-Genic Epistasis Model in F2 Populations -- Epistatic QTL Mapping Procedure in F2 Population -- Detection Power of Epistatic QTLs in F2 Populations -- Genetic Analysis and Detection Power of the Most Common Di-Genic Interactions -- Genetic Effects in Di-Genic Interactions -- Decomposition of Genetic Variance at the Presence of Di-Genic Epistasis. Power Simulation of Epistatic QTL Mapping -- Issues in Epistatic QTL Mapping -- Mapping of the QTL by Environment Interactions -- Mapping of the Additive QTL by Environment Interactions -- Mapping of the Epistatic QTL and Environment Interactions -- QTL and Environment Interactions in One Actual RIL Population in Maize -- Exercises -- Genetic Analysis in Hybrid F1 of Two Heterozygous Parents and Double-Cross F1 of Four Homozygous Parents -- Linage Analysis in the Hybrid F1 Derived from Two Heterozygous Parents -- Categories of Polymorphism Markers -- Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci -- Estimation of the Recombination Frequency Between Two Fully-Informative Markers -- Haploid Type Rebuilding in the Heterozygous Parents -- Estimation of the Recombination Frequency for Incompletely Informative Markers -- Theoretical Frequencies of Identifiable Genotypes Between the Complete Marker and Other Three Categories of Markers -- Theoretical Frequencies of Identifiable Genotypes Between Two Markers Belonging to Category II, III, or IV -- Theoretical Frequencies of Identifiable Genotypes Between Two Category IV Markers -- Haploid Type Rebuilding at the Presence of All Categories of Markers -- Linkage Analysis in Double Cross F1 Derived from Four Pure-Line Parents -- Marker Categories and Estimation of Recombination Frequency in the Double Cross F1 Population -- Equivalence Between the Double Cross F1 of Pure-Line Parents and Hybrid F1 of Heterozygous Parents -- Genotypic Frequencies at Three Complete Markers -- Imputation of Incomplete and Missing Marker Information -- QTL Mapping in the Double Cross F1 Population Derived from Four Pure-Line Parents -- One-QTL Genetic Model in Double Cross F1 Population -- The Linear Regression Model of the Phenotype on Marker Type for Multiple QTLs. Inclusive Composite Interval Mapping (ICIM) in the Double Cross F1 Population. 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. Description based on publisher supplied metadata and other sources. Genomics Mathematics. Génomique Mathématiques. SCIENCE / Life Sciences / Genetics & Genomics. bisacsh LI, Huihui. ZHANG, Luyan. Print version: 9782759830428 Current Natural Sciences Series. |
| spellingShingle | WANG, Jiankang Linkage Analysis and Gene Mapping. Current Natural Sciences Series. Intro -- Linkage Analysis and Gene Mapping -- Preface -- Contents -- Populations in Genetic Studies -- Commonly Used Populations in Genetic Studies -- Bi-Parental Populations -- Multi-Parental Populations -- Considerations in Developing Genetic Populations -- Preliminary Analysis of Genotypic Data -- Collection and Coding of Genotypic Data -- Gene Frequency and Genotypic Frequency -- Fitness Test on Genotypic Frequencies -- Genetic Effect and Genetic Variance -- Calculation of Population Mean and Phenotypic Variance -- One-Locus Additive and Dominance Model -- Population Mean and Genetic Variance at One Locus -- ANOVA on Single Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Single Environmental ANOVA on Rice Grain Length -- ANOVA on Multi-Environment Trials -- Linear Decomposition on Phenotypic Observation -- Decomposition of Sum of Squares of Phenotypic Deviations -- Multi-Environmental ANOVA on Rice Grain Length -- Estimation of Genotypic Values and the Broad-Sense Heritability -- Genotypic Values and Broad-Sense Heritability from Single Environmental Trials -- Genotypic Values and Broad-Sense Heritability from Multi-Environmental Trials -- Estimation of Genotypic Values Under Heterogeneous Error Variances -- Exercises -- Estimation of the Two-Point Recombination Frequencies -- Generation Transition Matrix -- Usefulness of the Transition Matrix in Linkage Analysis -- Transition Matrix of One Generation of Backcrossing -- Transition Matrix of One Generation of Selfing -- Transition Matrix of Doubled Haploid -- Transition Matrix of Repeated Selfing -- Expression of the Two-Locus Genotypic Frequencies in Matrix Format -- Theoretical Genotypic Frequencies at Two Loci -- Theoretical Frequencies of 10 Genotypes at Two Loci. Theoretical Frequencies of 4 Homozygotes in Permanent Populations -- Genotypic Frequencies of Two Co-Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Dominant Locus in Temporary Populations -- Genotypic Frequencies of One Co-Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Dominant Loci in Temporary Populations -- Genotypic Frequencies of One Dominant Locus and One Recessive Locus in Temporary Populations -- Genotypic Frequencies of Two Recessive Loci in Temporary Populations -- Estimation of Two-Point Recombination Frequency -- Maximum Likelihood Estimation of Recombination Frequency in DH Populations -- General Procedure on the Maximum Likelihood Estimation of Recombination Frequency -- Estimation of Recombination Frequency Between One Co-Dominant and One Dominant Marker in F2 Population -- Initial Values in Newton Algorithm -- EM Algorithm in Estimating Recombination Frequency in F2 Populations -- Effects on the Estimation of Recombination Frequency from Segregation Distortion -- Exercises -- Three-Point Analysis and Linkage Map Construction -- Three-Point Analysis and Mapping Function -- Genetic Interference and Coefficient of Interference -- Mapping Function -- Construction of Genetic Linkage Maps -- Marker Grouping Algorithm -- Marker Ordering Algorithm -- Use of the k-Optimal Algorithm in Linkage Map Construction -- Rippling of the Ordered Markers -- Integration of Multiple Maps -- Comparison of the Recombination Frequency Estimation in Different Populations -- LOD Score in Testing the Linkage Relationship in Different Populations -- Accuracy of the Estimated Recombination Frequency -- Least Population Size to Declare the Significant Linkage Relationship and Close Linkage -- Linkage Analysis in Random Mating Populations. Linkage Dis-Equilibrium in Random Mating Populations -- Generation Transition Matrix from Diploid Genotypes to Haploid Gametes -- Gametic and Genotypic Frequencies in Populations After Several Generations of Random Mating -- Exercises -- Single Marker Analysis and Simple Interval Mapping -- Single Marker Analysis -- Phenotypic Means of Different Genotypes at One Marker Locus -- Single Marker Analysis by t-Test in Populations with Two Genotypes -- Single Marker Analysis by t-Test in Populations with Three Genotypes -- ANOVA in Single Marker Analysis in Populations with Three Genotypes -- Likelihood Ratio Test in Single Marker Analysis -- Problems with Single Marker Analysis -- Simple Interval Mapping -- Frequencies of the QTL Genotypes in a Marker Interval -- Maximum Likelihood Estimation of Phenotypic Means of QTL Genotypes -- Testing for the Existence of QTL -- Estimation of Genetic Effects of QTL and Its Contribution to Phenotypic Variance -- Applications of Simple Interval Mapping in DH and F2 Populations -- Phenomenon of 'Ghost' QTL in Simple Interval Mapping -- Other Problems with Simple Interval Mapping -- Threshold Values of LOD Score in QTL Mapping -- Significance Level and Critical Value of One Test Statistic -- Distribution of the LRT Statistic at Single Scanning Positions in the Absence of Any QTL -- Factors Affecting the Distribution of the Genome-Wide Largest LOD Score -- Number of Effective Tests and the Empirical LOD Score Thresholds in QTL Mapping -- Permutation Test and the Empirical LOD Score Thresholds in QTL Mapping -- Exercises -- Inclusive Composite Interval Mapping -- Importance of the Control on Background Genetic Variation in QTL Mapping -- Inclusive Composite Interval Mapping in DH Populations -- Additive Genetic Model of One Single QTL -- Additive Genetic Model for Multiple QTLs. One-Dimensional Scanning and Hypothesis Testing for Additive QTLs -- Application of ICIM in a DH Mapping Population in Barley -- Inclusive Composite Interval Mapping in F2 Populations -- Additive and Dominant Model of One Single QTL -- Additive and Dominant Model for Multiple QTLs -- One-Dimensional Scanning and Hypothesis Testing in Additive and Dominant QTL Mapping -- Application of ICIM in an F2 Mapping Population -- Type II Error in Hypothesis Testing and Statistical Power in QTL Detection -- Type II Error and Statistical Power in Hypothesis Testing -- Probability of Two Types of Error and the Appropriate Sample Size -- Distribution and Effect Models of QTLs Used in Power Analysis by Simulations -- Calculation of the Detection Power and False Discovery Rate in QTL Mapping -- Comparison of IM and ICIM by Simulation -- QTL Detection Power and FDR from IM -- QTL Detection Power and FDR from ICIM -- Detection Powers Counted by Marker Intervals -- Suitable Population Size Required in QTL Mapping -- Avoiding the Overfitting Problem in the First Step of Model Selection in ICIM -- Exercises -- QTL Mapping for Epistasis and Genotype-by-Environment Interaction -- Epistatic QTL Mapping in DH Populations -- Linear Regression in Epistatic QTL Mapping and the Statistical Properties -- Two-Dimensional Scanning on Di-Genic Epistatic QTLs -- Genetic Variance on Epistatic QTLs with Linkage -- Simulation Study on Epistatic QTL Mapping in DH Populations -- Epistatic QTL Mapping in F2 Populations -- The Di-Genic Epistasis Model in F2 Populations -- Epistatic QTL Mapping Procedure in F2 Population -- Detection Power of Epistatic QTLs in F2 Populations -- Genetic Analysis and Detection Power of the Most Common Di-Genic Interactions -- Genetic Effects in Di-Genic Interactions -- Decomposition of Genetic Variance at the Presence of Di-Genic Epistasis. Power Simulation of Epistatic QTL Mapping -- Issues in Epistatic QTL Mapping -- Mapping of the QTL by Environment Interactions -- Mapping of the Additive QTL by Environment Interactions -- Mapping of the Epistatic QTL and Environment Interactions -- QTL and Environment Interactions in One Actual RIL Population in Maize -- Exercises -- Genetic Analysis in Hybrid F1 of Two Heterozygous Parents and Double-Cross F1 of Four Homozygous Parents -- Linage Analysis in the Hybrid F1 Derived from Two Heterozygous Parents -- Categories of Polymorphism Markers -- Unknown Linkage Phases in Heterozygous Parents and Genotypes in Their F1 Progenies at Two Loci -- Estimation of the Recombination Frequency Between Two Fully-Informative Markers -- Haploid Type Rebuilding in the Heterozygous Parents -- Estimation of the Recombination Frequency for Incompletely Informative Markers -- Theoretical Frequencies of Identifiable Genotypes Between the Complete Marker and Other Three Categories of Markers -- Theoretical Frequencies of Identifiable Genotypes Between Two Markers Belonging to Category II, III, or IV -- Theoretical Frequencies of Identifiable Genotypes Between Two Category IV Markers -- Haploid Type Rebuilding at the Presence of All Categories of Markers -- Linkage Analysis in Double Cross F1 Derived from Four Pure-Line Parents -- Marker Categories and Estimation of Recombination Frequency in the Double Cross F1 Population -- Equivalence Between the Double Cross F1 of Pure-Line Parents and Hybrid F1 of Heterozygous Parents -- Genotypic Frequencies at Three Complete Markers -- Imputation of Incomplete and Missing Marker Information -- QTL Mapping in the Double Cross F1 Population Derived from Four Pure-Line Parents -- One-QTL Genetic Model in Double Cross F1 Population -- The Linear Regression Model of the Phenotype on Marker Type for Multiple QTLs. Genomics Mathematics. Génomique Mathématiques. SCIENCE / Life Sciences / Genetics & Genomics. bisacsh |
| title | Linkage Analysis and Gene Mapping. |
| title_auth | Linkage Analysis and Gene Mapping. |
| title_exact_search | Linkage Analysis and Gene Mapping. |
| title_full | Linkage Analysis and Gene Mapping. |
| title_fullStr | Linkage Analysis and Gene Mapping. |
| title_full_unstemmed | Linkage Analysis and Gene Mapping. |
| title_short | Linkage Analysis and Gene Mapping. |
| title_sort | linkage analysis and gene mapping |
| topic | Genomics Mathematics. Génomique Mathématiques. SCIENCE / Life Sciences / Genetics & Genomics. bisacsh |
| topic_facet | Genomics Mathematics. Génomique Mathématiques. SCIENCE / Life Sciences / Genetics & Genomics. |
| work_keys_str_mv | AT wangjiankang linkageanalysisandgenemapping AT lihuihui linkageanalysisandgenemapping AT zhangluyan linkageanalysisandgenemapping |