| Foreword | p. v |
| Preface | p. vii |
| Introduction | p. 1 |
| Definitions | p. 1 |
| What is a 'good' genetic marker? | |
| Principal sources of molecular markers | p. 3 |
| Criteria of classification | p. 3 |
| Codominant markers detected individually | p. 4 |
| Sequence polymorphism | p. 4 |
| Differences at restriction enzyme sites: the RFLP technique | p. 5 |
| A particular case of RFLP: CAPS | p. 15 |
| Differences of conformation: SSCP | p. 17 |
| Differences of stability: D/TGGE | p. 17 |
| SNP genotyping techniques | p. 19 |
| Polymorphism of number of sequence repeats: SSR | p. 29 |
| Patterns of multiple dominant markers: genetic fingerprinting | p. 31 |
| Sequence polymorphism | p. 31 |
| Differences in hybridization sites of an arbitrary primer, or techniques of MAAP, RAPD, AP-PCR and DAF | p. 31 |
| Differences of restriction sites and hybridization sites of specific primers: AFLP | p. 35 |
| Polymorphism of number of tandem repeats | p. 37 |
| ISSR techniques | p. 37 |
| Minisatellites | p. 38 |
| Gene markers: cDNA and proteins | p. 39 |
| What markers are suitable for what purpose? | p. 39 |
| Glossary | p. 41 |
| Construction of genetic linkage maps | p. 47 |
| The concept of genetic distance | p. 48 |
| The Haldane distance | p. 49 |
| The Kosambi distance and other distances | p. 51 |
| Estimation of recombination rates and linkage tests | p. 53 |
| Comparing the most commonly used populations | p. 53 |
| Populations giving access to the haploid phase | p. 53 |
| Doubled haploids | p. 53 |
| Megagametophyte of gymnosperms | p. 56 |
| Backcross populations | p. 60 |
| F[subscript 2] populations | p. 61 |
| Recombinant inbred lines | p. 63 |
| Populations derived from non-fixed parents | p. 63 |
| General case | p. 66 |
| The double pseudo-testcross | p. 67 |
| Comparing the various types of populations | p. 68 |
| Perenniality | p. 68 |
| Estimation of dominance | p. 69 |
| Accuracy | p. 69 |
| Fundamentals of genetic maps | p. 72 |
| Saturation of maps | p. 72 |
| Relativity of map lengths | p. 74 |
| Relations between genetic and physical distances | p. 74 |
| Analysis of genome organization | p. 76 |
| Comparative mapping | p. 76 |
| Mapping of major genes | p. 81 |
| Approaches to mapping of major genes | p. 81 |
| Near-isogenic lines | p. 81 |
| Bulked segregant analysis (BSA) | p. 83 |
| Use of markers for cloning major genes | p. 85 |
| Principle of positional cloning | p. 85 |
| High-resolution mapping | p. 86 |
| Looking for the target gene in genomic clones | p. 86 |
| Mapping and characterization quantitative trait loci | p. 89 |
| Principle of QTL mapping | p. 92 |
| Detection of QTL considering markers individually | p. 93 |
| Finding QTL by analysis of variance in an F[subscript 2] population | p. 93 |
| Measurs of QTL effect | p. 99 |
| Limits of QTL detection on individual markers | p. 102 |
| Detection of QTLs from two or more markers | p. 102 |
| Methods of interval mapping | p. 102 |
| Multiple marker methods | p. 104 |
| Factors influencing QTL detection | p. 105 |
| Detection power and within-class variation | p. 105 |
| Population size and marker density | p. 106 |
| Choice of statistical risks | p. 107 |
| Deviation from normality | p. 107 |
| Advantages and disadvantages of populations currently used for QTL detection | p. 109 |
| Comparison of F[subscript 2], backcross, double haploids, and recombinant inbred lines | p. 109 |
| Progeny derived from heterozygous parents | p. 110 |
| Populations in which the genetic background is partly fixed | p. 110 |
| Selective genotyping | p. 111 |
| Genetic and molecular bases of quantitative trait variation | p. 112 |
| Genetic data on QTLs | p. 112 |
| QTLs are (almost) always detected | p. 112 |
| Dominance effects | p. 113 |
| Transgression | p. 113 |
| Epistasis | p. 114 |
| Genetic analysis of correlation between traits | p. 115 |
| Genetic dissection of traits | p. 117 |
| Effect of the environment | p. 117 |
| Comparative QTL mapping | p. 118 |
| Characterizing QTLs | p. 119 |
| QTL cloning | p. 119 |
| Candidate genes | p. 120 |
| Validation of candidate genes | p. 122 |
| Conclusion | p. 124 |
| Molecular markers in population genetics | p. 125 |
| Specific contributions of molecular markers in comparison to Traditional markers | p. 126 |
| Multialelism | p. 126 |
| Increase in the number of loci | p. 126 |
| Access to polymorphism of cytoplasmic DNA | p. 127 |
| Ordering of alleles | p. 127 |
| Analysis of molecular diversity | p. 129 |
| Measurement of nucleotide divergence from sequences | p. 129 |
| Measurement of nucleotide divergence using marker techniques | p. 130 |
| Polymorphism within a population | p. 133 |
| Expression of polymorphism within a population | p. 133 |
| Indexes taking into account the number of variants | p. 133 |
| Indexes taking into account the frequency of variants | p. 133 |
| Measurement of genetic diversity with different types of markers | p. 134 |
| At the allelic level | p. 134 |
| At the nucleotide level | p. 139 |
| Differentiation between populations | p. 140 |
| General expression of differentiation | p. 140 |
| Measurement of differentiation with different marker systems | p. 142 |
| At the allele level | p. 142 |
| At the nucleotide level | p. 143 |
| Gene flow | p. 143 |
| Indirect measures of gene flow | p. 146 |
| Comparative rates of seed and pollen migration | p. 146 |
| Origin of colonizing genotypes | p. 147 |
| Direct measures of gene flow | p. 148 |
| Conclusion | p. 149 |
| Application of markers in selection | p. 153 |
| Contribution of diversity studies to selection | p. 153 |
| Principal methods of data analysis | p. 154 |
| Relationships between molecular divergence, phenotypic divergence and coancestry | p. 155 |
| Application of classification methods: heterotic groups and genetic resource management | p. 156 |
| Relationship between molecular divergence and heterosis | p. 159 |
| Use of markers to protect new varieties | p. 163 |
| Perspectives | p. 163 |
| Marker-assisted selection | p. 164 |
| Genotype building | p. 164 |
| Marker-assisted backcrossing for a monogenic trait | p. 164 |
| Marker-assisted backcrossing for a polygenetic trait | p. 166 |
| Marker-assisted pedigree selection | p. 168 |
| Marker-assisted recurrent selection | p. 170 |
| Recurrent selection on markers alone | p. 170 |
| Recurrent selection on additive value predicted by markers | p. 170 |
| Combined selection based on phenotype and markers | p. 172 |
| Comparison with construction of genotypes | p. 175 |
| Choice between use of markers and increase in the number of replications | p. 175 |
| Conclusion | p. 176 |
| Appendix 1 | p. 177 |
| Appendix 2 | p. 180 |
| References | p. 185 |
| Index | p. 231 |
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