DNA Fingerprinting in Plants: Principles, Methods, and Applications, Second Edition

ISBN-13: 9780849314889 / Angielski / Miękka / 2005 / 472 str.

Kurt Weising; Kirsten Wolff; Hilde Nybom

Opis

Like its successful predecessor, this completely revised new edition serves as a comprehensive introduction to the field, as well as a handy reference for the researcher. Within the context of rapid advances in the field, the new edition focuses on PCR-based fingerprinting, including more sophisticated techniques. The description of the technology is complemented by a significant amount of background information. The new edition retains the extensive survey of applications of DNA fingerprinting in plants and a comparison of different types of molecular markers.

Spis treści

PREFACEREPETITIVE DNA: AN IMPORTANT SOURCE OF VARIATION IN EUKARYOTIC GENOMESCategories of DNA Sequence MutationsTandem-Repetitive DNA: The Biology of Mini- and MicrosatellitesMinisatellitesMicrosatellitesTransposable ElementsClass I TransposonsClass II TransposonsUnclassified TransposonsTransposons and Genome EvolutionTransposons as Molecular MarkersDETECTING DNA VARIATION BY MOLECULAR MARKERSProperties of Molecular MarkersTraditional Marker SystemsProtein Markers and AllozymesDNA SequencingRestriction Fragment Length Polymorphism (RFLP) AnalysisThe PCR Generation: Molecular Markers Based on In Vitro DNA AmplificationPrinciple of the PCRCleaved Amplified Polymorphic SequencesPCR with Arbitrary Primers: RAPD and Its VariantsMicrosatellitesInter-Repeat PCRDNA Profiling of Genic Regions: Resistance Gene Analog Polymorphism, Sequence-Related Amplified Polymorphism, and Target Region Amplification PolymorphismHybridization of Microsatellites to RAPD and MP-PCR ProductsAFLP Analysis and Its VariantsSingle-Strand Conformation Polymorphism Analysis and Related TechniquesMiscellaneous TechniquesLABORATORY EQUIPMENTMETHODOLOGYSafety PrecautionsIsolation, Purification, and Quantitation of Plant DNACollection and Preservation of Plant Tissue in the FieldPlant DNA Extraction: General ConsiderationsCTAB Protocol ICTAB Protocol IISDS-Potassium Acetate ProtocolDNA Preparation via NucleiQuantitation of DNABasic Molecular TechniquesRestriction of DNAPolymerase Chain ReactionDNA SequencingAgarose Gel ElectrophoresisPAA Gel ElectrophoresisDetection of DNA in GelsGel DryingSouthern BlottingGeneration of Radiolabeled Probes, Primers, and PCR ProductsBlot HybridizationSignal DetectionPCR with Arbitrary PrimersStandard RAPD ProtocolInfluence of Reaction Conditions and ComponentsModificationsMicrosatellite-Primed PCRStandard Protocol of Microsatellite-Primed PCRInfluence of Reaction Conditions and ComponentsModificationsPCR and Hybridization: Combinatory TechniquesAssessing the Genomic Copy Number of PCR AmpliconsTesting the Homology of Comigrating BandsRandom Amplified Polymorphic MicrosatellitesAmplified Fragment Length PolymorphismStandard AFLP Protocol Using RadioisotopesAFLP Protocol Using Fluorescence-Labeled PrimersSelective Amplification of Microsatellite Polymorphic Loci and Microsatellite AFLP ProtocolsTechnical Aspects and ModificationsRobustness and ReproducibilityGeneration and Analysis of Microsatellite MarkersMicrosatellite Analysis Using RadioisotopesMicrosatellite Analysis Using FluorochromesTechnical Aspects and ModificationsGenerating Microsatellite Markers Without CloningMicrosatellite CloningCAPS Analysis of cpDNA and mtDNAStandard CAPS ProtocolChoice of CAPS PrimersEVALUATION OF MOLECULAR MARKER DATARobustness and ReproducibilityReliabilityBand HomologyBand Linkage and NeutralityFragment Sizing and MatchingGeneral PrecautionsEquipmentMultilocus vs. Single-Locus ApproachesMultilocus MarkersSingle-Locus Markers and PolyploidsBand Sharing and Genetic DistancesCoefficients of SimilarityDissimilarity Coefficients and Genetic DistancesIdentity and UniquenessClonal StructureOrdination, Clustering, and DendrogramsOrdination TechniquesConstruction of DendrogramsPopulation Genetic AnalysisMeasures of VariationGenetic Differentiation between PopulationsGenetic Distances between PopulationsInbreeding Coefficient and Mating SystemsEstimation of Relatedness and Paternity TestingMigration and HybridizationGene Flow, Isolation-by-Distance, and Spatial StructurePhylogeography and Nested Clade AnalysisStatistical Testing of Hypotheses: Analytical and Computational Methods APPLICATIONS OF DNA FINGERPRINTING IN PLANT SCIENCESA Brief History of DNA FingerprintingMinisatellite and Oligonucleotide DNA Probes Detect Genetic VariationPCR-Based Methods Enter the StageMicrosatellite DNA Analyses Yield Codominant MarkersUniversal Organellar DNA Primers Produce Uniparental MarkersGenotype IdentificationIndividual-Specific DNA FingerprintsCultivar IdentificationIn Vitro-Propagated Plant Material and Somaclonal VariationSports and Other MutantsGenetic DiversityVariation and Relatedness among CultivarsAnalysis of Population Genetic Diversity and Its DistributionHybridization and IntrogressionPlant ConservationGermplasm Characterization and PreservationPlant Taxonomy and SystematicsTaxonomic Relationships Revealed by Multilocus DNA MethodsMicrosatellite Markers in Taxonomic StudiesTaxonomic Consequences from DNA Profiling Data PhylogeographyPhylogeography Based on cpDNAPhylogeography Based on Nuclear GenesLINKAGE ANALYSIS AND GENETIC MAPSGenerating High-Density Genetic MapsSelection of Parent PlantsMapping PopulationLinkage AnalysisThe Genetic MapCytogenetic MapsGenetic vs. Physical MapsSynteny: The Comparative Analysis of GenomesMarker-Assisted SelectionMolecular Markers and Positional CloningWHICH MARKER FOR WHAT PURPOSE: A COMPARISONMorphological Characters and Allozymes vs. DNA MarkersDifferent Kinds of DNA MarkersDiscriminatory PowerGenetic DistancesWithin- and Among-Population VariationGene Tagging and Genetic Linkage MappingCostsConclusionsFUTURE PROSPECTS: SNIPS AND CHIPS FOR DNA AND RNA PROFILINGSingle-Nucleotide PolymorphismsWhat Is a SNiPSNP DiscoveryDNA MicroarraysExpression Profiling and Expression MarkersAPPENDIX 1: PLANT DNA ISOLATION PROTOCOLSAPPENDIX 2: SUPPLIERS AND SELLERS OF REAGENTS AND EQUIPMENTAPPENDIX 3: COMPUTER PROGRAMS DEALING WITH THE EVALUATION OF DNA SEQUENCE VARIATION AND MOLECULAR MARKER DATAAPPENDIX 4: WEB PAGES OF INTERESTREFERENCESINDEX

O autorze

Kurt Weising, Hilde Nybom, Markus Pfenninger, Kirsten Wolff, Günter Kahl