BREEDING CROP PLANTS
1 BASIC INFORMATION ABOUT TOMATOES AND THE TOMATO GROUP 1 1 INTRODUCTION 1 2 ECONOMIC AND NUTRITIONAL IMPORTANCE OF TOMATO 1 2 1 ECONOMIC IMPORTANCE 1 2 2 NUTRITIONAL COMPOSITION 1 3 ACADEMIC IMPORTANCE OF TOMATO AND ITS WILD RELATIVES 1 3 1 TOMATO AS A MODEL SPECIES 1 3 1 1 THE GENETIC BASIS OF QUANTITATIVE TRAITS 1 3 1 2 FRUIT DEVELOPMENT 1 3 2 THE TOMATO CLADE AS A MODEL SYSTEM 1 3 2 1 PLANT DEFENSE 1 3 2 2 MATING SYSTEM AND SPECIATION 1 3 2 3 ADAPTATION AND DIVERGENCE 1 4 TAXONOMY AND EVOLUTION 1 4 1 TAXONOMIC POSITION AND PHYLOGENETIC RELATIONSHIPS 1 5 BOTANICAL DESCRIPTIONS 1 5 1 MORPHOLOGY 1 5 2 PLOIDY LEVELS, GENOME SIZE AND KARYOTYPE 1 6 ECOLOGY AND BIODIVERSITY OF THE TOMATO CLADE 1 6 1 DISTRIBUTION AND HABITATS 1 6 2 MATING SYSTEM EVOLUTION IN THE TOMATO CLADE 1 6 2 1 MATING SYSTEM DIVERSITY 1 6 2 2 THE GENETIC BASIS OF MATING SYSTEM DIVERSITY 1 6 3 GENETIC DIVERSITY IN WILD TOMATOES 1 6 3 1 GENETIC DIVERSITY AND MATING SYSTEM 1 6 3 2 GENETIC DIVERSITY AND GEOGRAPHY IN SI SPECIES 1 6 3 3 GENETIC DIVERSITY AND GEOGRAPHY IN SC SPECIES CONTENTS 1 7 TOMATO DOMESTICATION AND DISSEMINATION 1 8 TOMATO BREEDING AND RESEARCH RESOURCES 1 8 1 GENETIC RESOURCES 1 8 1 1 MUTANT STOCKS 1 8 1 2 MAPPING LINES 1 8 1 3 WILD AND CULTIVATED GERMPLASM 1 8 2 GENOMIC RESOURCES 1 8 3 BIOINFORMATIC RESOURCES REFERENCES 2 CLASSICAL GENETICS AND TRADITIONAL BREEDING 2 1 INTRODUCTION 2 2 CLASSICAL MAPPING EFFORTS WITH MORPHOLOGICAL AND ISOZYME MARKERS 2 3 LIMITATIONS OF CLASSICAL ENDEAVORS AND UTILITY OF MOLECULAR MAPPING 2 4 CLASSICAL TOMATO BREEDING ACHIEVEMENTS 2 4 1 DISEASE RESISTANCE 2 4 2 QUANTITATIVELY INHERITED TRAITS AND CULTIVARS—PROCESSING TOMATOES 2 4 3 QUANTITATIVELY INHERITED TRAITS AND CULTIVARS—FRESH MARKET TOMATOES 2 4 4 QUALITATIVE INHERITANCE 2 4 5 ALLOZYMES 2 4 6 STRESS TOLERANCE 2 4 7 ACHIEVEMENT EFFORTS 2 5 BREEDING OBJECTIVES POSITIVE AND NEGATIVE 2 5 1 HISTORICAL BACKGROUND 2 5 2 JOINTLESS PEDICELS 2 5 3 PARTHENOCARPY 2 5 4 HIGH PIGMENT 2 5 5 FRUIT DISORDERS 2 5 6 FLAVOR 2 5 7 LARGE FRUIT SIZE 2 5 8 MULTIPLE DISEASE RESISTANCE 2 5 9 GENETIC BACKGROUNDS 2 5 10 ENVIRONMENTAL VARIATION/STRONG G X E INTERACTIONS 2 5 11 COMBINING ABILITY 2 6 LIMITATIONS OF TRADITIONAL BREEDING AND RATIONALE FOR MOLECULAR BREEDING ACKNOWLEDGEMENTS 3 DIVERSITY WITHIN CULTIVATED TOMATO 3 1 INTRODUCTION 3 2 PHENOTYPIC ANALYSIS OF TOMATO FRUIT 3 3 THE EFFECT OF THE TOMATO SHAPE GENES ON FRUIT MORPHOLOGY 3 4 GENOTYPE-BASED DIVERSITY ANALYSIS 3 5 GENETIC DIVERSITY WITHIN CULTIVATED TOMATO GERMPLASM 3 6 FUTURE PROSPECTS ACKNOWLEDGEMENTS 4 MOLECULAR MARKERS, GENETIC MAPS AND ASSOCIATION STUDIES IN TOMATO 4 1 INTRODUCTION 4 2 MOLECULAR MARKERS FOR TOMATO GENOME MAPPING AND MARKER/TRAIT ASSOCIATION STUDIES 4 2 1 RFLPS AND RFLP-BASED PCR MARKERS 4 2 2 PCR-BASED ANONYMOUS MARKERS 4 2 3 MICROSATELLITE OR SSR MARKERS 4 2 4 SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MARKERS 4 3 GENETIC MAPS AND AVAILABLE MARKERS 4 4 POPULATION STRUCTURE, LINKAGE DISEQUILIBRIUM AND ASSOCIATION OF MARKERS AND TRAITS 4 4 1 POPULATION STRUCTURE IN TOMATO 4 4 2 LINKAGE DISEQUILIBRIUM 4 4 3 FIRST EFFORTS TOWARDS ASSOCIATION MAPPING IN TOMATO 4 4 4 CANDIDATE GENE ANALYSIS 4 5 FUTURE DEVELOPMENTS 4 5 1 REQUIREMENTS ON MARKERS FOR MARKER/TRAIT ASSOCIATIONS 4 5 2 LARGE SCALE SNP IDENTI? CATION FOR MARKER/TRAIT ASSOCIATIONS 4 5 3 GENOME-WIDE ASSOCIATION STUDIES 4 5 4 THE FUTURE—THE TOMATO GENOME SEQUENCE, LARGE SCALE PHENOTYPING AND ASSOCIATION STUDIES ACKNOWLEDGEMENTS 5 MAPPING AND TAGGING OF SIMPLY INHERITED TRAITS 5 1 INTRODUCTION 5 2 IMPORTANCE OF THE SIMPLY INHERITED TRAITS 5 3 GENETIC AND MOLECULAR DISSECTION OF SIMPLY INHERITED TRAITS 5 4 IDENTI? CATION OF MARKERS LINKED TO TRAITS OF INTEREST 5 4 1 USE OF NILS TO IDENTIFY LINKAGE WITH MOLECULAR MARKERS 5 4 2 USE OF BULKED SEGREGANT ANALYSIS (BSA) TO IDENTIFY LINKAGE WITH MOLECULAR MARKERS 5 4 3 CONVERSION OF DOMINANT TO CODOMINANT MARKERS 5 5 USE OF GENOMICS TOOLS FOR MAPPING 5 6 SIMPLY INHERITED TRAITS ASSOCIATED WITH FRUIT NUTRITIONAL QUALITY 5 7 SIMPLY INHERITED TRAITS ASSOCIATED WITH FRUIT TASTE BRIX, SUGARS, ACIDS AND AROMA VOLATILES 5 8 SUMMARY 6 MOLECULAR MAPPING OF COMPLEX TRAITS IN TOMATO 6 1 INTRODUCTION 6 2 POPULATIONS USED FOR QTL MAPPING 6 2 1 PRIMARY SEGREGATING POPULATIONS 6 2 2 RECOMBINANT INBRED POPULATIONS 6 2 3 ADVANCED BACKCROSS POPULATIONS 6 2 4 BACKCROSS INBRED LINES 6 2 5 INTROGRESSION LINES 6 3 FRAMEWORK MAPS AND MARKERS 6 4 QTL MAPPING APPROACHES AND SOFTWARE 6 5 INTROGRESSION LINE MAPPING AND BREEDING APPROACH 6 5 1 INTROGRESSION LINE HETEROSIS 6 6 INTERACTIONS BETWEEN QTL AND GENETIC BACKGROUND 6 7 MAS AND QTL PYRAMIDING 6 8 MENDELIZING QTLS 6 9 QTL MAPPING ON A TRAIT BASIS 6 9 1 DISEASE RESISTANCE 6 9 1 1 VIRAL RESISTANCE 6 9 1 2 BACTERIAL RESISTANCE 6 9 1 3 FUNGAL RESISTANCE 6 9 2 INSECT RESISTANCE 6 9 3 ABIOTIC STRESS TOLERANCE 6 9 3 1 COLD TOLERANCE 6 9 3 2 DROUGHT TOLERANCE 6 9 3 3 SALT TOLERANCE 6 9 4 FRUIT YIELD 6 9 5 FRUIT QUALITY 6 9 5 1 FRUIT WEIGHT 6 9 5 2 FRUIT SHAPE 6 9 5 3 FRUIT COLOR 6 9 5 4 FRUIT FIRMNESS 6 9 5 5 PRIMARY METABOLIC TRAITS 6 9 5 6 SUGAR AND ACID CONTENT 6 9 5 7 NUTRITIONAL AND ANTIOXIDANT COMPOUNDS 6 9 5 8 VOLATILE COMPOUNDS 6 9 5 9 SENSORY TRAITS 6 9 6 FLOWERING AND RIPENING TIME 6 9 7 FLOWER MORPHOLOGY AND REPRODUCTIVE BARRIERS 6 9 8 LEAF, SEPAL, AND PETAL MORPHOLOGY 6 9 9 SEED WEIGHT 6 10 CONCLUSIONS AND FUTURE PROSPECTS ACKNOWLEDGMENTS 7 MOLECULAR BREEDING 7 1 INTRODUCTION 7 2 GERMPLASM CHARACTERIZATION AND EXPLOITATION 7 2 1 PRE-BREEDING 7 2 2 TESTING FOR DISTINCTNESS, UNIFORMITY AND STABILITY (DUS) 7 2 3 HYBRID PURITY TESTING 7 3 MARKER-ASSISTED TRAIT INTROGRESSION 7 3 1 GENE AND QTL INTROGRESSION 7 3 2 GENE PYRAMIDING 7 3 3 GENETIC IDEOTYPE BREEDING 7 4 ADVANTAGES, LIMITATIONS AND PROSPECTS OF MAS 7 4 1 ADVANTAGES 7 4 2 LIMITATIONS AND SOLUTIONS 7 4 2 1 UNAVAILABILITY OF CLOSELY-LINKED MARKERS FOR MANY TRAITS 7 4 3 PROSPECTS FOR MAS 7 4 3 1 FROM “MAS” TO “GAS” 7 5 TRANSGENIC BREEDING 7 5 1 TRAITS AND OBJECTIVES 7 5 1 1 SUGARS 7 5 1 2 CAROTENOIDS 7 5 1 3 VIRUS RESISTANCE 7 5 1 4 PARTHENOCARPY 7 5 1 5 FRUIT FIRMNESS 7 5 1 6 PROLONGED VINE LIFE 7 5 2 PERSPECTIVES 7 6 CONCLUDING REMARKS ACKNOWLEDGEMENT 8 POSITIONAL CLONING STRATEGIES IN TOMATO 8 1 INTRODUCTION 8 2 MUTANT COLLECTIONS 8 3 STRATEGIES FOR GENERATING MAPPING POPULATIONS 8 4 STRATEGIES FOR EXTRACTING DNA FOR GENETIC MAPPING 8 5 MOLECULAR MARKERS 8 6 ASSIGNING LOCI TO CHROMOSOMAL REGIONS 8 7 FINE GENETIC MAPPING 8 8 RESOURCES FOR GENERATING PHYSICAL MAPS 8 9 IDENTI? CATION AND CON? RMATION OF CANDIDATE GENES 8 10 THE IMPACT OF AN EMERGING GENOME SEQUENCE 8 11 ALTERNATIVE STRATEGIES FOR IDENTI? CATION OF MUTANT LOCI 8 12 FUTURE PERSPECTIVES 9 STRUCTURAL GENOMICS: STUDYING VARIATION IN GENE SEQUENCES 9 1 INTRODUCTION 9 2 SOURCES OF SEQUENCE 9 2 1 EXPRESSED SEQUENCE TAGS 9 2 1 1 SOURCES OF ESTS 9 2 2 GENE SPACE 9 3 TARGETED MARKER DISCOVERY 9 3 1 THE BASIS OF DNA MARKERS 9 3 2 ANNOTATED SEQUENCE 9 3 3 CATEGORIZING ESTS FOR MARKER DISCOVERY 9 3 4 DIVERSITY OF TOMATO ESTS 9 3 4 1 DIVERSITY IN THE GENE SPACE OF TOMATO 9 3 4 2 MINING FOR VARIATION 9 3 4 3 ESTS AS TEMPLATES 9 3 5 THE NEXT GENERATION OF DISCOVERY 9 4 CONCLUSION 10 THE TOMATO GENOME SEQUENCING PROJECT 10 1 INTRODUCTION 10 2 SEQUENCING STRATEGY 10 2 1 BAC BY BAC APPROACH 10 2 2 WHOLE GENOME SHOTGUN 10 3 GENOME ANNOTATION BY ITAG 10 4 CONCLUSION 11 COMPARATIVE GENOME SEQUENCING OF TOMATO AND POTATO: METHODS AND ANALYSIS 11 1 INTRODUCTION 11 2 A PIPELINE FOR THE COMPARATIVE SEQUENCING OF TOMATO AND POTATO GENOMES 11 3 ADVANTAGES OF COMPARATIVE GENOME SEQUENCING 11 3 1 IMPROVING THE PHYSICAL MAPS 11 3 2 SELECTING ADDITIONAL SEED BACS 11 3 3 BENE? TS TO BAC FINISHING 11 4 COMPARATIVE ANALYSIS OF SYNTENIC CLONES OBTAINED FROM COMPARATIVE SEQUENCING 11 4 1 CHARACTERIZATION OF SYNTENIC SEQUENCES 11 4 2 COLINEARITY BETWEEN TOMATO AND POTATO 11 4 3 CONTENT AND DISTRIBUTION OF REPETITIVE ELEMENTS 11 4 4 INSERTED OR DELETED (INDEL) GENES WITHIN SYNTENIC REGIONS 11 4 5 DIVERGENCE OF SYNTENY LENGTH BETWEEN TOMATO AND POTATO 11 5 LIMITATIONS AND OPPORTUNITIES 12 DEVELOPMENTS IN TOMATO TRANSCRIPTOMICS 12 1 INTRODUCTION 12 2 TRANSCRIPTOMICS TOOLS DEVELOPED 12 2 1 MICROARRAYS 12 2 2 SAGE AND RELATED TECHNOLOGIES 12 2 3 MASSIVE PARALLEL SIGNATURE SEQUENCING 12 3 ADVANCES IN SEQUENCING TECHNOLOGIES 12 3 1 454 GENOME SEQUENCER FLX 12 3 2 ILLUMINA 12 3 3 ABI SOLID SEQUENCING 12 3 4 THIRD GENERATION AND OTHER SEQUENCING TECHNOLOGIES 12 3 5 RNA-SEQ 12 4 BIOINFORMATIC CHALLENGES AND DATA ANALYSIS 12 5 USE OF RELATED SPECIES RESOURCES 12 6 APPLICATION OF FUNCTIONAL GENOMICS IN GENOMICS-ASSISTED BREEDING 12 7 SUMMARY 13 PROTEOMICS AND METABOLOMICS 13 1 INTRODUCTION 13 2 TOMATO PROTEOMICS: TECHNIQUES, APPLICATIONS, AND QTL ANALYSES 13 2 1 PROTEOMICS METHODS 13 2 1 1 PROTEIN EXTRACTION 13 2 1 2 TRADITIONAL 2DE-BASED METHODS 13 2 1 3 MASS SPECTROMETRY 13 2 1 4 SHOTGUN PROTEOMICS 13 2 1 5 ANALYSIS OF POST-TRANSLATIONAL MODI? CATIONS 13 2 1 6 PROTEIN COMPLEXES 13 2 2 APPLICATION OF PROTEOMICS TO FUNCTIONAL STUDIES 13 2 2 1 FRUIT DEVELOPMENT AND RIPENING 13 2 2 2 ABIOTIC STRESS 13 2 2 3 BIOTIC STRESS 13 2 3 PROTEOMICS AND QTL MAPPING 13 2 3 1 PATHOGEN RESISTANCE 13 2 3 2 FRUIT QUALITY TRAITS 13 3 TOMATO METABOLOMICS: TECHNIQUES, APPLICATIONS, AND QTL ANALYSES 13 3 1 METABOLOMICS TOOLS 13 3 1 1 METABOLITE EXTRACTION 13 3 1 2 GC-MS 13 3 1 3 LC-MS 13 3 1 4 CE-MS 13 3 1 5 NMR 13 3 1 6 ANALYTICAL STRATEGIES 13 3 2 APPLICATION OF METABOLOMICS TO FUNCTIONAL STUDIES 13 3 2 1 COMPREHENSIVE ANALYSIS OF TOMATO FRUIT METABOLITES 13 3 2 2 TISSUE-DEPENDENT ACCUMULATION OF METABOLITES 13 3 2 3 METABOLOME ANALYSIS IN TRANSGENIC TOMATO PLANTS 13 3 3 METABOLOMICS AND QTL MAPPING 13 3 3 1 METABOLIC PRO? LING OF WILD SPECIES 13 3 3 2 METABOLIC PRO? LING OF ILS BETWEEN S PENNELLII AND S LYCOPERSICUM 13 4 APPLICATION IN PHENOMICS-ASSISTED BREEDING 13 4 1 INTEGRATED -OMICS 13 4 2 DATABASES 14 ROLE OF BIOINFORMATICS AS A TOOL IN TOMATO RESEARCH 14 1 INTRODUCTION 14 2 GENE AND GENOME DATABASES 14 2 1 INTERNATIONAL TOMATO GENOME SEQUENCING PROJECT 14 2 2 SOLANUM LYCOPERSICUM PLANT GENOME DATABASE (SLGDB) 14 2 3 SOLANACEAE GENOMICS RESOURCE 14 2 4 TOMATO GENOME PROJECT AT NCBI 14 2 5 C M RICK TOMATO GENETICS RESOURCE CENTER (TGRC) 14 2 6 GENES THAT MAKE TOMATOES 14 2 7 REAL-TIME QTL (RTQ) 14 2 8 OTHER PLANT RESOURCES 14 3 COMPARATIVE GENOME DATABASES 14 4 GENE EXPRESSION DATABASES 14 4 1 TOMATO GENE INDEX (AT DFCI) 14 4 2 TOMATO FUNCTIONAL GENOMICS DATABASE (TFGD) 14 4 3 KAZUSA MICRO-TOM DATABASE (MIBASE) 14 4 4 KAZUSA FULL-LENGTH TOMATO CDNA DATABASE (KAFTOM) 14 4 5 AFFYMETRIX GENECHIP® TOMATO GENOME ARRAY 14 4 6 RNA-SEQ 14 4 7 APPLICATIONS 14 5 MOLECULAR MARKER AND GENETIC MAP DATABASES 14 5 1 MAPS 14 5 1 1 GENETIC MAPS 14 5 1 2 PHYSICAL MAP 14 5 1 3 CYTOLOGICAL MAP 14 5 1 4 SEQUENCE PROGRESS MAP 14 5 1 5 OTHER MAPS 14 5 2 TRANSPOSON TAGGING 14 5 3 TARGETING INDUCED LOCAL LESIONS IN GENOMES (TILLING) 14 6 PROTEIN AND METABOLOME DATABASES 14 6 1 TOMATO METABOLITE DATA AT TFGD 14 6 2 SECRETOM 14 6 3 OTHER PLANT RESOURCES 14 6 4 APPLICATIONS 14 7 INTEGRATION OF DIFFERENT DATA TYPES 14 7 1 THE SOL GENOMICS NETWORK (SGN) 14 7 2 SOLANACEOUS MAPMAN 14 7 3 FRUIT BIOLOGY LABORATORY AT INRA BORDEAUX 14 7 4 MIPSPLANTSDB 14 7 5 OTHER RESOURCES 14 7 6 APPLICATIONS 14 8 CONCLUSIONS BASIC INFORMATION ABOUT TOMATOES AND THE TOMATO GROUP ABSTRACT DOMESTICATED TOMATO, SOLANUM LYCOPERSICUM, IS BOTH AN ECONOMICALLY IMPORTANT CROP SPECIES AND A RESEARCH MODEL ORGANISM TOMATOES ARE AMONG THE MOST WIDELY CONSUMED VEGETABLES IN THE WORLD, AND MANY OF THE COMPOUNDS FOUND IN TOMATOES HAVE RECEIVED MUCH INTEREST IN RECENT YEARS FOR THEIR POTENTIAL HEALTH BENE? TS DUE TO ITS SHORT GENERATION TIME AND SIMPLE GROWING REQUIREMENTS, CULTIVATED TOMATO HAS BEEN USED IN SCIENTI? C RESEARCH FOR MORE THAN A HUNDRED YEARS, SERVING AS A MODEL FOR FRUIT DEVELOPMENT, AND FOR ELUCIDATING THE GENETIC BASIS OF QUANTITATIVE VARIATION CULTIVATED TOMATO IS PART OF A CLADE OF ~13 CLOSELY RELATED WILD SPECIES, WHICH HAVE ALSO BEEN INSTRUMENTAL IN THE DEVELOPMENT OF THE CROP AS A MODEL SYSTEM WILD TOMATOES ARE A RICH SOURCE OF GENETIC AND MORPHOLOGICAL DIVERSITY, AND BECAUSE MOST SPECIES CAN BE CROSSED WITH CULTIVATED TOMATO, THEY HAVE PLAYED A ROLE IN THE GENERATION OF VARIOUS GENETIC AND BREEDING RESOURCES ADDITIONALLY, STUDY OF THE WILD SPECIES THEMSELVES HAS CONTRIBUTED TO OUR UNDERSTANDING OF MATING SYSTEM EVOLUTION, PLANT DEFENSE, AND HOW PLANT SPECIES ADAPT AND DIVERGE ALTHOUGH QUESTIONS REMAIN ABOUT THE EXACT PHYLOGENETIC RELATIONSHIPS AMONG WILD TOMATOES, AND ABOUT THE HISTORY OF TOMATO DOMESTICATION, THE CONCERTED EFFORTS CARRIED OUT BY THE TOMATO RESEARCH COMMUNITY TO CREATE ACCESS TO VARIOUS GENETIC, GENOMIC, GERMPLASM, AND BIOINFORMATICS RESOURCES FURTHER CONTRIBUTES TO THE DEVELOPMENT OF THIS SPECIES AS A MODEL SYSTEM