Insect Resistance

Tomatoes (S. lycopersicum) are susceptible to a wide array of arthropod pests (Lange and Bronson 1981 Berlinger 1986 Kennedy 2003). Currently available cultivars do not have sufficiently high levels of pest resistance to allow for significant reductions in the amount of pesticides used in the crop. Consequently, developing cultivars with increased levels of pest resistance is a major focus of some breeding programs, along with their adoption into integrated pest management programs aimed at...

Fusarium Wilt

Fusarium wilt causes major crop losses worldwide. Currently, there are three races (races 1, 2, and 3) of the causal organism Fusarium oxysporum f. sp. lycop-ersici. Yellow older leaves are the first symptoms of the disease, this is followed by entire branches turning yellow, but often only one side or part of a leaf or branch will turn yellow. When the outer part of the vascular tissue is examined a characteristic red brown discoloration can be found which extends up into the plant. This...

DNA Library Creation

Appropriate tissue collection and subsequent purification of genomic DNA from each M2 plant is essential for successful recovery of the mutations induced during mutagenesis. In many plant species, tissue collection must be done at a young developmental stage to optimize quantity, quality, and purity of DNA. Sampling of older or damaged tissue should be avoided as it can adversely affect the quality and long-term stability of the extracted DNA. In tomato, high quality DNA can be extracted from...

Cultivarsand Landraces

The TGRC maintains a collection of 198 modern and vintage cultivars, inbreds, and breeding lines for various purposes, kept mainly to provide isogenic (or nearly isogenic) stocks for specific mutants, standards for genetic comparison, sources of disease resistances, or other purposes. Another 226 cultivated tomato accessions are Latin American landraces assembled from various sources, mainly collected from local markets in Latin American. Much larger collections of cultivars are preserved at...

Bioinformatics

A comprehensive bioinformatics infrastructure is a critical resource for tomato researchers. Databases, websites, and associated tools allow fast and easy access to data such as sequences, annotation, mapping and expression information. This enables rapid progress and the generation of new hypotheses (Rhee et al. 2006). As one of the central genetic model systems of the Asterid clade, a large number of websites and informatics tools are available for tomato. The ongoing tomato genome sequencing...

Comparative QTL

There are several examples of successful comparative QTL mapping in the Solanaceae. Much of the comparative QTL mapping has been done with fruit Fig. 6. Determination of marker orthology by map position. In this example, CD422 is located between TG766 and TG922 in the tomato genome. CD422 hybridizes to two fragments in the pepper genome that map to different loci. CD422b in pepper is designated orthologous to CD422 in tomato due to its similar map position. CD422a is paralogous Fig. 6....

Metabolic Annotation

Metabolite annotation aims to collect and integrate as much information as possible from a given metabolite peak to provide information as to its identity and structure. Although there is no consensus as to the total number of tomato metabolites, 73 and 555 metabolites are registered in the categories Lycopersicon and Solanum, respectively, in the metabolite database Dictionary of Natural Products (http www.chemnetbase.com scripts dnpweb.exe welcome-main) as of March 2007. In two separate...

Evolution of Fruit Color

Three variable characters within the tomato clade have garnered much attention in attempts to understand evolutionary dynamics of the group. The most obvious of these characters is the evolution of carotenoid pigments affecting fruit color. Fruit color of wild tomatoes varies from green to red, orange, and yellow. Various studies have demonstrated that green fruit is the ancestral character and that colored fruit arose once within the clade (e.g., Palmer and Za-mir 1982 Miller and Tanksley 1990...

Drought Responsive Genes

By screening samples using microarrays, approximately 130 drought responsive genes were identified in Arabidopsis (Reymond et al. 2000 Seki et al. 2001). These drought responsive genes were placed into functional classes using the predicted amino acid sequence of the gene to identify possible gene functions drought responsive genes were found in eleven of the 13 possible functional classes (Bray 2002). A search of GenBank (March 2007) for drought responsive genes returned the following numbers....

Fruit Firmness QTLs

Firmness is an important trait for fruit quality. It is related to shelf-life and to fruit texture, and thus has been frequently measured in genetic studies. Several long shelf-life mutants have contributed to the understanding of fruit maturation (Giovannoni 2001, 2004 Seymour et al. 2002). The first to be described, Never ripe (Nr, Rick 1956) was the first cloned (Wilkinson etal. 1995). The Nr gene encodes a protein homologous to ETR1 in Arabidopsis. ETR1 is an ethylene receptor, explaining...

QTL Characterization Finemapping Positional Cloning and Candidate Genes

When a QTL is mapped within a genomic region, this implies that there is at least one gene responsible for a fraction of the phenotypic variation. Before trying to identify the gene responsible for the QTL, it first must be precisely characterized at the genetic level. It is critical to determine the number of QTLs segregating within the region. Indeed, several fine-mapping experiments identified several QTLs in regions where a single QTL was detected or where it was assumed that a single gene...

Drought Responsive H1 Histone

The association of H1 histones with nucleosomal arrays is believed to be primarily responsible for the formation ofhigher orders of chromatin compaction, thus inactivating the transcription of genes in that chromatin region. The family of plant H1 histones can be divided into two groups based on size, amino acid sequence, and expression characteristics (As-cenzi and Gantt 1997). The larger group, equivalent to the somatic linker histones in animals, is comprised of the H1 histones associated...

Metabolomics Databases

The most reliable class of metabolite annotation is provided when chemical information of an observed metabolite matches known compounds in natural product databases or descriptions from the literature. Moco etal. (2006) reported an analysis of fruit extracts pooled from 96 cultivars representing three major fruit types (cherry, Dutch beef, normal round) using LC-Q-TOF-MS. They annotated metabolites using m z, retention time, absorption spectra, and MS MS data and performed database searches...

Fruit Color and Nutritional Value

There is a wealth of genetic variability within modern and heirloom tomato cultivars, landraces, and wild species for improvement of fruit nutritive value. Progress in breeding for improved tomato nutritional value is largely influenced by availability of sufficient genetic diversity and knowledge of gene action. Breeding strategies for improved nutritional composition are similar to those for other traits in a cultivar development program. Based on knowledge gained through investigations of...

Ab initio and in silico Discovery of SSR Indel and SNP Markers Without a priori Knowledge of Map Position

The identification of tomato SSRs and SNPs was greatly improved once sufficient sequence database resources became available. In particular, large collections of expressed sequence tags (ESTs) hosted in various databases greatly facilitated molecular marker development (Table 5). In the first attempt at in silico marker discovery for tomato, the search for SSRs by computational screening of genomic sequences from EMBL and GenBank databases resulted in the identification and confirmation of 36...

Tomato

Labate1, Silvana Grandillo2, Theresa Fulton3, St phane Munos4, Ana L. Caicedo5, Iris Peralta6, Yuanfu Ji7, Roger T. Chetelat8, J. W. Scott7, Maria Jose Gonzalo9, David Francis9, Wencai Yang9, Esther van der Knaap9, Angela M. Baldo1'10, Brian Smith-White11, Lukas A. Mueller12, James P. Prince13, Nicholas E. Blanchard13, Dylan B. Storey13, Mikel R. Stevens14, MatthewD. Robbins9, Jaw-Fen Wang15, Barbara E. Liedl16, Mary A. O'Connell17, John R. Stommel18, Koh Aoki19, Yoko Iijima19, Ann J....

Bacterial Canker

Few studies have been conducted to evaluate the degree of variation of bacterial canker caused by Clavibacter michiganensis subsp. michiganensis. Strains of C. michiganensis subsp. michganensis were highly genetically similar (> 80 ) based on repetitive-sequence-based PCR (rep-PCR) fingerprinting (Louws etal. 1998). Nonetheless, the pathogen could be grouped into four distinct genetic types designated A through D. Studies on mapping for resistance have used strains that were either highly...

Reverse Genetic Strategies in Tomato

The increasing abundance of gene sequence information in tomato and other plants is giving rise to new opportunities for studies of gene function. In a traditional forward genetic approach, a phenotype is investigated to determine the underlying genetic basis of atrait. Inareversegenetic approach, theaimistoalter a gene or its expression level in order to study the resulting phenotype. Ideally, a reverse genetic approach allows a genome wide interrogation of genes, so that the function of every...

TED httptedbticornelledu

The Tomato Expression Database is the primary database for tomato microarray data (Fei et al. 2006). The database consists of three parts (1) the tomato Microarray Data Warehouse, serving as the central repository for raw gene expression data and experimental descriptions in a minimal information about a microarray experiment (MIAME) compliant format (2) the Tomato Microarray Expression Database, storing the processed experimental results from a number of fruit development time course...

Tobacco Nicotiana tabacum

The first genetic linkage map for the cultivated tetraploid tobacco was recently published (Bindler et al. 2007). For this work, SSR primers were identified through sequences provided by the Tobacco Genome Initiative (http www.tobaccogenome.org), and 293 loci were successfully mapped. In addition to the Tobacco Genome Initiative, there is a European effort, the European Sequencing of Tobacco project (http www.estobacco.info). Previous mapping had been done in members of the genus other than...

Metabolomics and Molecular Breeding

Metabolomics facilitates the deduction ofbiologically relevant hypotheses as to putative metabolic pathways and genes responsible for metabolic reactions. The assignment of candidate genes for crop improvement will be accelerated as the body of tomato genomic data increases. High-throughput metabolic profiling holds vast potential for screening promising tomato genes, varieties, and species for metabolite-oriented molecular breeding (Fig. 13). Firstly, profiling of complex secondary metabolites...

Bacterial Spot

Molecular breeding for tomato bacterial spot caused by Xanthomonas spp. has been constrained by several factors. First, four species and five races of the pathogens have been described. The causal agents include X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (race T3, T4, T5), and X. gardneri (race T2) (Jones et al. 2004,2005). Secondly, resistance traits in several known sources are quantitatively inherited. Thirdly, the three resistance sources Hawaii 7998, Hawaii 7981,...

Creating a Tilling Population Mutagenesis

A TILLING population with a high mutation frequency will maximize efficient mutation detection and minimize the number of individuals that need to be screened to find mutations. For example, screening an 1 Kb gene in a population of 5,000 individuals with an average mutation frequency of 1 mutation per 250 Kb yields about 20 mutations in Arabidopsis (Greene et al. 2003). There is an approximately 60 chance that one of these 20 mutations will be a knockout (Henikoff et al. 2004). Increasing the...

Genetics and Salt Stress Resistance Characteristics in Tomato Species

Several species of tomato are sources of salt resistance S. pimpinellifolium, S. cheesmaniae, S. galapagense, S. pennellii and S. peruvianum (reviewed in Flowers 2004 Foolad 2004 Cuartero et al. 2006). As with drought, salt stress may have more than one definition, and resistance or tolerance to salt depends on the developmental stage of the plant (Foolad and Lin 1997). There are several possible physiological processes or components of salt tolerance and mapping of QTL for salt tolerance in...

Potyvirus

Potato virus Y (PVY) and Tobacco etch virus (TEV) are in the Potyvirus genus and belong to the family Potyviridae. PVY has had strain specific resistance reported making it difficult to widely use resistant germplasm (Nagai et al. 1992 Green and Hanson 1996 Legnani et al. 1997). Resistance has been reported in S. habrochaites and S. pimpinellifolium (Nagai et al. 1992 Stobbs et al. 1994 Green and Hanson 1996 Legnani et al. 1997 Thomas andMcGrath 1988). From these studies only one gene was...

Begomoviruses

Tomato chlorotic mottle virus (TCMV), ToMoV, and TYLCV are members of the Begomovirus genus (family Geminiviridae). These three viruses, for which resistance genes in tomato have been described, are among at least 35 viruses in this genus (Fauquet et al. 2003). These whitefly vectored viruses can be divided into two groups, those with a monopartite or bipartite genome (Ji etal. 2007). The cultivated tomato has provided little resistance to these viruses (Pico et al. 1998 Ji etal. 2007). The...

Corky Rot

Corky root rot is caused by Pyrenochaeta lycopersici Schn. & Ger. and causes root lesions that form a corky textureprogressively destroyingtherootsystem(Ger-lach and Schneider 1964). Resistance in the form of a recessive gene, py-1, has been integrated into culti-vars from S. peruvianum (Laterrot 1983) and is found on the short arm of chromosome 3 between markers TG40 and CT31 (Doganlar et al. 1998). A new source of resistance controlled by a single dominant gene was reported by Stamova...

Wild Species

The TGRC collections include over 1,000 accessions of wild species representing 9 to 13 species - depending on the taxonomic system used - in Solanum sect. Lycopersicon, and four related Solanum species (Chetelat 2004). Detailed passport information is available for each accession at the TGRC website (http tgrc.ucdavis.edu). In addition, 458 and 659 accessions of wild species, the majority ( 71 ) of which are S. peruvianum and S. pimpinellifolium, are preserved at USDA-PGRU (http...

Preface to the Volume

Vegetables include a versatile group of crop plants. Tomato, eggplant or Capsicums are botanically fruits but traditionally they are treated as vegetables and with due respect to the convention, we have included them in Volume 5 dedicated to vegetables. On the other hand, we could have included crops such as cowpea, pea and potato in this volume however, they found place in Volume 3 representing pulses, sugar and tuber crops. Beets could also have appeared in Volume 3 for they include sugar...

Volatile Compounds QTLs

QTLs for volatile compounds have been mapped in two populations. Saliba-Colombani et al. (2001) detected QTLs for 12 volatile compounds among 18 that were quantified in the progeny of a cross between cherry tomato inbred line Cervil and larger-fruited inbred line Levovil. Tieman et al. (2006) identified QTLs for 23 volatiles in the population of ILs derived from S. pennellii. Twenty-five loci altered in content of one or more volatiles were identified. Although ten volatiles were analyzed in...

Potexvirus

Both Pepino mosaic virus (PepMV) and Potato virus X (PVX) are in the Potexvirus genus in the Flex-iviridae family. PepMV was first reported in greenhouse tomatoes in Europe in 1999 (van der Vlugt et al. 2000) and has since been found in tomatoes of North and South America (French etal. 2001 Soler etal. 2002). Pico etal. (2002) reported that S. chilense and S. habrochaites both indicated resistance to PepMV. At this time, there is no published report as to the incorporation of this resistance...

Detection

MS is the primary detection method for plant metabolomic analysis. GC-MS is applicable to detect volatile metabolites (e.g., alcohols, monoterpenes, esters), and also non-volatile polar metabolites (primary metabolites, e.g., amino acids, sugars, lipids, organic acids). Metabolites can be identified by comparing fragment peak patterns and retention indices with those of standard compounds in databases. LC-MS is a versatile technology to analyze non-volatile secondary metabolites. However, in...

Phenotypic Analysis

Depending on the goals of the investigator, the desired phenotype can be a disruption of function to aid in basic research of a largely uncharacterized gene, or it can be to achieve a specific goal, such as improved agronomic or fruit quality traits. In either case, background mutations are the largest hurdle for any investigator in acquiring a clean phenotype. Fig. 14. Example of a 96-lane TILLING assay used for detection of mutations in 6-fold pools of tomato DNA. A gel image from the IRD 700...

Extraction

Optimum extraction conditions differ for different types of metabolites. To extract carbohydrates, amino acids, and fatty acids from tomato tissues using GC-MS, an extraction protocol originally developed for potato tuber (Roessner et al. 2000) has been widely used. To extract secondary metabolites for non-targeted analysis by liquid chromatography MS (LC-MS), a methanol extraction has been widely applied (Bino et al. 2005 Moco et al. 2006). A lipophilic solvent (e.g., chloroform) is required...

Mating System Evolution

Two additional characters of wild tomatoes, self-incompatibility (SI) and allogamy (i.e., mating system), have played an important role in the evolution of the clade. SI is an ancestral character in the tomato clade (Rick et al. 1977 Miller and Tanksley 1990), and loss of SI has occurred independently several times. Notably, SI hasbeenlostinsomepopulationsof S. pennellii (Rick and Tanksley 1981), some populations of S. habrochaites (Rick et al. 1979), and in the clade containing colored-fruited...

Strategies

The continued genetic improvement of crop species depends on the introgression of new alleles. Thus, it is imperative that new tools and concepts be developed that would allow the more efficient use of the genetic potential stored in gene banks and in exotic germplasm. Here we review two related molecular breeding strategies the Advanced Backcross QTL (AB-QTL) method and the Introgression Line (IL) strategy. These have been developed and tested in tomato as well as several other crops with the...

Alternaria Stem Canker

Alternariastem canker caused by Alternaria alternata f. sp. lycopersici was first reported in California, but is now found in many tomato production areas (Gro-gan et al. 1975). Dark brown to black cankers form on infected plants near the soil line or just above the ground. This disease can girdle and destroy the plant. Foliar and fruit symptoms may also occur. Alternaria stem canker resistance is controlled by a single dominant gene designated Asc, which is incompletely dominant to a...

Cucurbits

Dean, J. E. Staub 10.1.1 Origin and 10.1.2 Cucurbit Production 10.2 Genetic Mapping of Cucurbit 10.3 Genetic Mapping of Mendelian 10.3.1 Fusarium Wilt 10.3.2 Mapping of Other Resistance 10.3.3 Fruit Flower 10.4 Genetic Mapping of Quantitative Traits 10.5 Marker-Assisted Selection (MAS) 10.6 Map-Based Cloning 10.7 Cucurbit Genetic 10.8 Future J. McCallum 11.1.1 Taxonomy and 11.1.2 Genetic Resources and 11.1.3 Cytology and Genome 11.2 Molecular Markers and Other...

Drought or Water Deficit Stress Resistance Summary

The genetic basis for abiotic stress resistances and tolerances in wild tomato species are quantitatively inherited consequently it is unlikely that a single transgene expressed in cultivated tomato will confer agronomically relevant drought or salt tolerance. A complete understanding of the biochemical and physiological basis of abiotic stress resistances is essential for the development of crops able to yield har-vestable product, i.e., tomato fruit, when grown with reduced water or poor...

Cytological and Cytogenetic Maps

Tomato aneuploid stocks have been used as tools for mapping loci for many decades (Lesley 1932). Populations developed from crosses between irradiated and mutant cultivars were extensively used to generate chromosome-based maps of tomato in the 1960s (Khush and Rick 1967b, 1968a, b) (Table 7, map 1). Radiation-induced chromosomal deficiencies allowed expression of recessive mutant alleles and localized mutations to chromosomal arms. In the 1990s, a resurgence of interest in cytology prompted...

Principles of QTL Mapping

Molecular markers allow the analysis of the genetic control of quantitative traits by mapping QTL. Mapping QTL is based on a systematic search for association between the genotype at a marker locus and the average value of a phenotypic trait. It requires a segregating population, e.g., derived from the cross between two individuals with different values of the trait of interest. For each individual within the population, the genotype of marker loci distributed over the entire genome is...

Early Blight

The fungus Alternaria solani causes the disease early blight and is found worldwide in locales with frequent rainfall or heavy dew. Early blight lesions are characterized by concentric rings of brown or black giving a classic target appearance. In addition, a yellow area surrounds the spots which coalesce to engulf the entire leaf, stem, or fruit. Initial efforts focused on incorporating stem resistance, particularly collar rot resistance from S. lycopersicum (Andrus etal. 1942), but also...

Blackmold

A mold of ripe fruit, blackmold, is caused by the fungus Alternaria alternata and can lead to severe harvest losses in processing tomatoes (Pearson and Hall 1975). The disease progression begins with dry sunken lesions on the fruit which may extend into fruit cavities. RAPD genotyping of A. alternata identified two major phenetic groups and genetic diversity of the pathogen (Morris et al. 2000). QTLs for blackmold resistance were mapped by Robert et al. (2001) and found on chromosomes 2, 3, 9,...

Analysis of Mutations

Once the exact nucleotide change of a mutation is known through sequencing, online programs can be used to predict the effect on the encoded protein. One such program is called PARSESNP (Project Aligned Related Sequences and Evaluate SNPs) (Taylor and Greene 2003). This program uses the supplied reference DNA and mutation sequence information to locate and determine if the nucleotide change alters the protein sequence. The PARSESNP program also compares the sequence of the gene of interest to...

Mutation Discovery via Tilling

To increase the efficiency of the high-throughput screening process, DNA samples in a 96-well format are pooled together, allowing as many as 576 to 768 individuals to be screened simultaneously with 6-fold or 8-fold pooling. After pooling, PCR is used to amplify regions of target genes for mutation screening. With few exceptions, gene-specific primers are required for efficient mutation discovery. Primers that amplify more than one gene typically lead to decreased assay efficiency due to...

Ab initio Discovery of Indel and SNP Markers Without a priori Knowledge of Map Position

One disadvantage to developing SSR or SNP markers in transcribed sequences is their low polymorphism between closely related tomato species and within cultivated germplasm. The sequence of coding regions is more conserved than non-coding regions. Therefore, the design of primers corresponding to the 5' or 3' UTR provides one approach to increase the chance for polymorphic SSR, indel or SNP detection (Cato et al. 2001). Another approach for detection of polymorphisms is to mine intron sequences....

Carbohydrates

Considerable research effort has been dedicated to improving tomato fruit solids content because of the influence of solids on fruit quality (Stevens 1986). Sugars comprise 55 to 65 of the total soluble solids fraction and approximately 50 of the total solids in tomatoes. Considerable variability for soluble solids concentration is present within the cultivated tomato and its wild relatives. Soluble solids concentration of commercial hybrid cultivars generally ranges from 4.5 to 6.0 and can...

Genetic Engineering of Stress Resistance

Many genes whose expression is increased in response to drought or salt stresses have been cloned and characterized (Plant et al. 1991 Torres-Schumann et al. 1992 Chen et al. 1993,1994 Fray et al. 1994 Yu et al. 1996 Trevino and O'Connell 1998 Harrak et al. 2001 Tirajoh et al. 2005 Yesbergenova et al. 2005). Transgenic expression of these genes has been used for two different objectives, to determine the function of the protein or gene product in the stress response or to attempt to confer...

Economic Importance

Tomato is a major vegetable crop, has gained in popularity over the last century, and is now grown in almost every country of the world (Robertson and Labate 2007). Worldwide production of fresh market and processing tomatoes has steadily increased during the last decade and reached an annual production of 124.4 million tons in 2004, with an average yield of 27.5 ton hectare (Table 2 FAOSTAT 2004). The tomato growing area has increased by 38 and production by 42 worldwide in the past 10 years....

Fruit Weight and Fruit Shape QTLs

Grandillo et al. (1999) summarized the results of QTL mapping for fruit weight obtained in 17 studies based on progeny of various types and involving seven wild species. According to the studies, three to more than 18 QTLs were detected. Six QTLs explained more than 20 of the phenotypic variation. A common set of 28 QTLs could be identified that frequently segregated in at least two populations. Nevertheless only QTL cloning and complementation permits determination of whether each consensus...

International Tomato Genome Sequencing Project

The International Tomato Genome Sequencing Project is a consortium of groups from ten different countries, including the USA, whose goal is to sequence the euchromatic regions of each of the 12 tomato chromosomes. The USA group is sequencing three of the chromosomes (1,10,11) and the remaining nine chromosomes are each being sequenced by a group from a different country. The breakdown on the countries sequencing the remaining nine chromosomes is as follows Korea - chromosome 2, China -...

Late Blight

Phytophthora infestans, an oomycetes close to fungus, causes late blight worldwide on both tomato and potato. Conditions conducive to development of the disease include cool temperatures and cloudy weather, which if ideal, can destroy the crop within a few days. Wild species are the source for high levels of resistance to late blight in both Solanaceous crops. Currently three named genes are being used in tomato breeding Ph-1 (Bonde and Murphy 1952 Gallegly 1952), Ph-2 (Turkensteen 1973...

Principles of QTL Mapping and Characterization

In tomato, many important traits are under mono-genic control (e.g., disease resistance, fruit color, shelf life, determinate growth). Molecular markers have been used to map and characterize these loci for decades and are frequently used by breeders for rapid screening of disease resistance genes. The availability of saturated molecular genetic maps of tomato has facilitated QTL mapping for traits related to fruit characteristics and yield, and for adaptation to abi otic stresses. Tomato is...

Metabolomics Data Collection

Tomato contains a diverse range of metabolites with different molecular weights and polarities (Fig. 11). Thus, itiscurrently notpossibletoobtainanoverview of the entire metabolome in a single analysis. Never theless, it has been shown that metabolite analyses with comprehensive coverage, if not complete, can provide novel insights into plant metabolic pathways (Urbanczyk-Wochniak et al. 2003 Hirai et al. 2004, 2005 Tohge et al. 2005). Comprehensive coverage is achieved through combinations of...

Future Approaches for Marker Development

Irrespective of the goal, genetic analyses of tomato continue to require development of markers. Thanks to the efforts of the International Tomato Sequencing Project (see Sect. 1.18) (Mueller et al. 2005b) and the Potato Genome Sequencing Consortium (Table 5), sequence information from these two species will substantially increase in the near future and significantly facilitate marker development. Additional sequence information from other tomato varieties and its wild relatives will also...

Springer

Chittaranjan Kole Department of Horticulture 316 Tyson Building The Pennsylvania State University University Park, PA 16802 USA Library of Congress Control Number 2006933735 ISBN-13 978-3-540-34535-0 Springer Berlin Heidelberg New York This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other...

Molecular Characterization of QTLs for Quality

Molecular characterization of QTLs consists of identifying the corresponding genes and the variation of either DNA sequence or gene expression explaining trait variation. High throughput genomic approaches can facilitate this by providing candidate genes for QTLs based on gene function. High throughput methods (transcriptomics, proteomics, metabolomics) allow the identification of changes in the content of mRNAs, proteins or metabolites by comparing two or more samples. First applied in...

Tospoviruses

Tomato spotted wilt virus (TSWV), which is vectored by at least ten species of thrips (Whitfield et al. 2005), is the type species of the genus Tospovirus (family Bunyaviridae) and was the only tospovirus name recognized until the early 1990s. Related tospo species that infect tomato include Groundnut bud necrosis virus (GBNV Folkertsma et al. 1999), Groundnut ringspot virus (GRSV Boiteux and Giordano 1993), and Tomato chlorotic spot virus (TCSV Boiteux and Giordano 1993). Tospoviruses infect...

Potato S tuberosum

The first RFLP map of potato was published by Bonier-bale etal. (1988), which first delineated the five inversions that characterize the differences between lo cus order in the tomato and potato genomes. Other groups subsequently published potato maps and compared them to tomato (e.g., Gebhardt et al. 1991). The high-density linkage map developed by Tanksley et al. (1992) for tomato remains an excellent resource for potato genetics, because a large number of orthol-ogous markers were placed on...

Solanaceae Comparative Mapping Future Prospects

Comparative mapping proceeds at a rapid pace within the Solanaceae, because any mapping project that uses markers previously used in other mapping projects can be linked to those previous projects. The ultimate form of comparative mapping, comparative sequencing, is increasingly becoming feasible, with significant sequencing efforts being devoted to many members of the Solanaceae. As this book goes to press, approximately 19 of the tomato nuclear genome has been sequenced by the members of the...

Carotenoids

Consumption of tomato products is associated with decreased risk of cardiovascular disease and certain cancers, including prostate and cervical cancer (Gio-vannucci et al. 1995 Gerster 1997 Clinton 1998 Gio-vannucci 1999 Paiva and Russell 1999). P-carotene is well recognized as a pro-vitamin A carotenoid. More recent discussions note the positive association between lycopene and health, but also emphasize that there are a family of beneficial compounds in tomato (Laquatra et al. 2005). Lack of...

Markers

RFLPs were used to generate the first high-density linkage maps in tomato (Bernatzky and Tanksley 1986 Tanksley etal. 1992) (see Sect. 1.5) but are not amenable to high-throughput and automated genotyping analyses. AFLP markers alleviated the throughput limitations of RFLPs, but are largely anonymous, population-specific, and dominant (Haanstra etal. 1999). Sequence-dependent PCR based markers are preferred over RFLP and AFLP, and are now exploited in many plant species. These markers display...

TIGR httpwwwtigrorg

The Institute for Genomics Research (TIGR) maintains a database of plant sequences and transcript assemblies called Plant TA (http plantta.tigr.org). This database contains sequences for several tomato species and provides transcript assemblies for other Solanaceous plants (Childs et al. 2007). In the past TIGR maintained the Plant Gene Indices database, but this database has since moved to the Computational Biology and Functional Genomics Laboratory at Harvard (http compbio.dfci.harvard.edu ).

Fruit Quality Conclusions

Tomato quality is a complex character due to its number of components and because it is dependent on conditions throughout the entire process of plant and fruit development. Genetic variation for fruit quality is extensive, especially if one considers the possibilities offered by wild tomato species. A few mutations have been shown to be involved in fruit quality, particularly in ripening, and QTL studies have revealed anumberofgenomic regionsinvolvedinthe variation of quality traits. Several...

Insoluble Solids

Tomato fruit insoluble solids contribute to fruit viscosity and firmness. Insoluble solids are comprised of water insoluble solids (WIS) and alcohol insoluble solids (AIS), the former being slightly larger. A strong relationship exists between AIS and viscos ity, with fruit pericarp accounting for high correlation coefficients (Janoria and Rhodes 1974). The inheritance of AIS in a cross of high and low AIS cultivars demonstrated high heritability (0.68 and 0.75), additive genetic variation, and...

Cytogenetic Stocks

The tomato genome is well represented by various types of cytogenetic stocks. The TGRC maintains au-totetraploids, sesquidiploids, translocations, and several types of trisomics. These stocks contain cyto-logically detectable changes in chromosome numbers or chromosome structure. The autotetraploids and sesquidiploids are euploids (i.e., have changes in whole sets of chromosomes), while the trisomics are aneuploids, having a single extra chromosome which maybe rearranged in various ways. The...

Fruit Quality

For processing tomato, fruit soluble solids content, pH, and paste viscosity are the major quality traits. According to distributors and retailers, fruit quality is essentially defined by shelf-life and firmness. During recent years, these criteria have been taken into account for breeding but have led to flavorless fruit. For consumers, quality is defined by the traits governing fruit attractiveness and fruit flavor. Nutritional quality (e.g., antioxidants, vitamins) is also important (See...

Mutants

The TGRC collection includes more than 1,000 monogenic mutants at over 600 loci, including spontaneous and induced mutations affecting many aspects of plant development and morphology, disease resistance genes, protein marker stocks, and other traits of economic importance (Chetelat 2005). Genetic data on individual stocks, including phenotypes, images, chromosome locations, etc. are available at the TGRC website. An additional series of provisional (i.e., less well characterized) mutants are...

Reverse Genetics and Tilling Conclusions

Sensitive mutation discovery by TILLING is opening up new prospects for functional genomics in a wide array of crops, especially those for which sequence information is limited or those in which transformation is not available or efficient. Some of the plants in which TILLING has been reported include Arabidop-sis, lotus, wheat, maize, rice, barley, poplar, and soybean, with the list continuing to grow (Gilchrist and Haughn 2005 Hohmann et al. 2005 Slade and Knauf 2005 Comai and Henikoff2006)....

Brief History of Comparative Mapping

Comparative mapping in plant genomes originated in the Solanaceae, through the early work of Tanksley and colleagues (Bernatzky and Tanksley 1986 Bonier-bale et al. 1988 Tanksley et al. 1988). In these studies, isozyme and RFLP markers were placed onto maps of tomato and its close relatives within the Solanaceae, pepper, and potato (Solanum tuberosum). Orthology of loci, or identity by descent from a common ancestral sequence, was determined based on map position. For example, if a tomato...

Anthracnose Ripe

Anthracnose ripe rot is a common disease caused by Collelotrichum coccodes and other Colletotrichum species (Barksdale 1972). Fruit exhibiting anthrac-nose symptoms have sunken, dark, circular lesions on ripe fruit. This disease is primarily found on processing tomatoes grown in humid regions. Resistance was first reported in 1964 (Robbins and Angell 1970) as partially dominant and polygenic. However an F2 population studied by Stommel and Zhang (1998, 2001) identified three regions associated...

Sugar and Acid Content QTLs

Chromosomal regions carrying QTLs for sugar content or related traits (Brix , fructose, glucose, or sucrose content), based on 14 populations involving eight different species (Patersonet al. 1988,1990,1991 Azanza et al. 1994 Eshed and Zamir 1995 Goldman etal. 1995 Grandillo and Tanksley 1996b Tanksley etal. 1996 Fulton etal. 1997, 2000, 2002a Bernacchi etal. 1998b Chen etal. 1999 Saliba-Colombani et al. 2001 Doganlar et al. 2002c Causse et al. 2004 Frary et al. 2004) are summarized in Fig. 7....

Gray Leafspot

A complex of four species of the fungus Stemphyl-lium S. solani, S.floridanum, S. botryosum,and S. vesi-carum, are responsible for gray leafspot. These fungi are found worldwide on tomatoes and exhibit similar symptoms. Shiny, smooth and gray lesions are found on the underside of leaves and later the foliage has a shot hole appearance. In severe cases, leaves turn yellow, this is followed by leaf drop, and in some cases, defoliation of the entire plant. A single incompletely dominant gene,...

Advancedbackcross and Introgressionline Breeding Future Prospects

The processes of plant domestication and plant breeding have produced crops which exhibit characteristics that humans appreciate high yield, good flavor, and large edible parts. However, these same processes have led to the diminished genetic variability of many cultivated species, leaving them vulnerable to new diseases and pests and making further improvements impossible without the input of new variation. The results obtained from the AB-QTL and IL strategies applied in tomato as well as in...

Micronutrients

Considerable genetic variation exists in tomato for micronutrients with antioxidant activity or other health conferring properties (Hanson et al. 2004 Schauer et al. 2005). A number of these micronutrients, particularly carotenoids, have long been major objectives of breeding programs because of their contribution to the quality of fresh and processed tomato products. Increased recognition of their health promoting properties has stimulated new research to identify loci that influence their...

Lipids

Phytosterols are important structural components of plant membranes and stabilize phospholipid bilay-ers in plant cell membranes. Moreau et al. (2002) and Piironen et al. (2000) have recently reviewed phytos-terols in foods and their health promoting properties. Phytosterols have received increased attention in the last 10 years because of their cholesterol-lowering properties. The primary interest in tomato phytos-terols has focused on ripening related events involving phospholipids and their...

Growing a Tilling Population

After determining the mutagenic treatment that gives ahigh mutation frequency suitable for screening without widespread lethality or sterility, a large population (> 10,000) of M1 plants is typically cultivated to provide sufficient numbers of plants for efficient TILLING (McCallum et al. 2000b). In the specific case of tomato, growing the M1 plants in the field at commercial densities, instead of in the greenhouse, is usually more economical. This is especially true because the M1 generation...

Leaf Mold

Leaf mold is a disease problem found generally in protected culture due to the high humidity requirements of the pathogen, Cladosporium fulvum. Older leaves show the yellowish light-green blotches first, followed by a purplish or olive green mold on the lower side of the leaves coupled with a yellowing on the upper leaf surface. Lower leaves of infected plants will eventually turn yellow and drop off. Spread of the fungus is gen-erallyvia the air or transportbyworkers or irrigation water...

SSRsand Indels

For SSRs and indels, large polymorphisms between 20 bp to 1 kb can be detected using agarose gel elec-trophoresis. Fragment size differences from two to 20 bp are typically detected on polyacrylamide gels. The fragment separation can be performed by elec-trophoresis on non-denaturing polyacrylamide gels and stained with ethidium bromide or silver. One apparatus to perform this task is the vertical sequencer DASG-400 to DASG-600 (CBS SCIENTIFIC, California, USA). The throughput of this system is...

Fruit Quality MAS

A marker-assisted backcross scheme was set up for introducing favorable alleles of five major QTL regions into three tomato lines with common taste (Lecomte et al. 2004a). The results demonstrated the usefulness of such an approach for improving fruit quality. In all three genetic backgrounds, the introduced regions had a favorable effect on the traits controlled by QTLs from the cherry tomato (donor line), with the exception of fruit weight. Consumer tests revealed that the prototypes were...

Metabolomics

A major goal of tomato metabolomics is to elucidate genes and biosynthetic pathways that can be exploited for crop improvement in productivity and quality. Tomato productivity involves net accumulation of photosynthetically synthesized compounds such as sugars and amino acids, and polymeric compounds derived from them, e.g., cellulose and starch. Fruit quality is determined by a complex blend of traits including taste, fragrance, and color. These traits are mostly attributed to metabolite...

Sensory Traits QTLs

Certain cherry tomato accessions have been shown to be most flavorful among tomato cultivars. In order to study organoleptic quality through all of its components, a QTL experiment was designed using the progeny of a cherry tomato line (Cervil, with high quality fruit) and a classical inbred line for fresh market (Levovil, producing large fruit with a common taste) (Causse et al. 2001, 2002 Saliba-Colombani et al. 2001). A population of 144 RILs was developedfrom crossingthese two lines....

Stability of QTL Over Environment

The environment may have a significant impact on the effect of QTL a QTL detected in one environment may no longer be detected in another, or its effect may vary in magnitude (see Sect. 1.8.2). This has been frequently observed, although environmental influence differs according to the characters and the range of environments studied (Paterson et al. 1991). Certain QTLs are detected in all or almost all environments tested, while others are specific to a single environment. Several statistical...

Marker Development Leveraging Public Databases and Software Tools

Despite extensive availability of tomato molecular markers, many markers were developed based on polymorphism in wide crosses and are not informative when used within closely related germplasm. For example, whereas a saturated linkage map of tomato is available from a wide cross, S. lycopersicum x S. pen-nelli (Fulton et al. 2002b), populations derived from crosses of closely related species and crosses within S. lycopersicum require substantial additional effort to construct molecular linkage...

Preface to the Series

Genome science has emerged unequivocally as the leading discipline of this new millennium. Progress in molecular biology during the last century has provided critical inputs for building a solid foundation for this discipline. However, it has gained fast momentum particularly in the last two decades with the advent of genetic linkage mapping with RFLP markers in humans in 1980. Since then it has been flourishing at a stupendous pace with the development of newly emerging tools and techniques....

Brassica oleracea

Ziolkowski, J. 8.1.1 Brief History of the 8.1.2 Botanical 8.1.3 Economic 8.1.4 Breeding 8.1.5 Classical Mapping 8.1.6 Classical Breeding Achievements 8.2 Construction of Genetic 8.2.1 First Generation 8.2.2 Second Generation 8.2.3 Comparative 8.3 Gene 8.4 Brassica oleracea Quantitative Trait Loci (QTL) 8.4.1 Resistance to Plasmodiophora 8.4.2 Transformation and Plant 8.4.3 Developmental 8.5 Marker-Assisted 8.6 Map-Based Cloning 8.7 Advanced 8.7.1 Comparative...

PCRbased Linkage Map of S lycopersicum cv Rio Grande x S pimpinellifolium LA1589 F2 Population

The development of a reference genetic map covering the entire genome with PCR-based markers demonstrates how public resources can be used to facilitate genetic investigations of tomato populations. Frary et al. (2005) reported on the first sequence-dependent PCR-based map for tomato for a population derived from a cross between S. lycopersicum and S. pennellii. Using many of the techniques reviewed above, a set of 87 PCR-based markers were mapped between two much more closely related...

SGN httpsgncornelledu

The SOL Genomics Network (SGN) (Mueller et al. 2005a), the front end website of the SOL project, is a comprehensive resource based on the clade-oriented database (COD) principle. Essentially, data from an entire clade of organisms is integrated into the database rather than data from a single model species. This allows more meaningful integration of diverse datasets for different organisms in a comparative and phylogenetic context. In this vein, SGN contains extensive comparative mapping data,...

Base Substitutions

Detection of nucleotide changes that don't result in size differences requires other assays for detection. Cleaved amplified polymorphic sequence (CAPS) offer a convenient method of detection when the SNP alters a recognition site for a restriction enzyme (Konieczny and Ausubel 1993). After PCR amplification, fragmentsare cutwiththe restrictionenzyme that specifically digests one of the alleles. The digestion fragments are then separated on an agarose gel and scored. However, CAPS are limited...

Minerals

The role of minerals in plant foods that have a positive effect on human health are well established (Lachance 1998). Tomato mineral composition is greatly influenced by plant nutrition, and as a result, has been well characterized in the context of mineral deficiency and the effect of these conditions on plant health. There is significant genotypic variation for mineral content in tomato fruit. Potassium, together with nitrate and phosphorous, constitutes approximately 93 of the total...

Isolation of Fruit Quality QTL

Fine mapping experiments that allow the precise mapping of QTL within a chromosomal region is the first step towards positional cloning (Paterson et al. 1990 Fraryet al. 2003b Lecomte et al. 2004b). Fine mapping may reveal the existence of several linked QTLs. For example, Lecomte et al. (2004b) identified two linked QTLs with moderate effects for fruit weight within a 20 cM region that were confounded as one major effect QTL. Correspondence of map location of QTLs and genes related to carbon...

Taxonomic Placement

Traditionally, wild and cultivated tomatoes have been considered within the genus Lycopersicon in the Solanaceae family, mainly based on the typical androceum where the anthers are connivent laterally to form a flask-shaped cone with an elongated sterile tip at the apex. However, there has been considerable flux in the taxonomy of tomatoes in the last 450 years. Early European botanists recognized the close relationship of tomatoes with the genus Solanum, and commonly referred to them as S....

Dispersal

The Spanish distributed the most desirable vegetables and fruit throughout their empire. From Central America and Mexico, the Spanish introduced the tomato into the Caribbean and the Philippines. From the Philippines, use of tomato spread to Southeast Asia and ultimately the rest of Asia (Smith 1994). Through the Spaniards the tomato was also taken back to Spain and disseminated throughout Europe. The earliest mention of tomato in European literature appeared in a document written by an Italian...

Tomato Future Prospects

Since the early years when the first genetic markers were identified as being linked to disease resistance in tomato, there have been steady increases in developing molecular markers for genome mapping and MAS for numerous traits. Public and private sector breeders, as well as molecular marker service-providing companies, have placed increasing demands for new markers linked to additional genes influencing disease, pest, and abiotic stress resistances, fruit quality including flavor and...

Phenolic Compounds

Flavonoids, phenolic acids, and polyphenols are the main classes of dietary phenolics (King and Young 1999). Flavonoids, which include anthocyanins, are the largest group of plant phenols and have been the subject of considerable research since they impart color to many horticultural commodities. Vinson etal. (1998) determined that vegetables high in phenolic compounds have antioxidant quality superior to that of the antioxidant vitamins A, C and E. In a survey of S. lycopersicum and S....

Germplasm Collections

A wide range of germplasm resources are available for breeding and research on tomato (see recent reviews Table 2. World production of tomatoes in 1995 and 2004 (FAOSTAT 2004) Table 2. World production of tomatoes in 1995 and 2004 (FAOSTAT 2004) by Chetelat and Ji 2007 Ji and Scott 2007 Robertson and Labate 2007). Tomato germplasm collections in the USA are currently maintained at two major genebanks, the C.M. Rick Tomato Genetics Resources Center (TGRC), at the University of California -...

Amino Acids

Variability for reported amino acid composition in tomato fruit is likely due to both genotypic differences and plant nutrition (Davies 1966a Freeman and Woodbridge 1960). Interest in amino acid content of tomato has generally focused upon their influence on fruit flavor. Attempts to influence fruit amino acid composition have been limited to studies evaluating the effect of different fertilizer regimes (Carangal et al. 1954 Davies 1964). Glutamic, a-aminobutyric, glutamine, and aspartic...

Genetic Engineering

Development of methods to transfer genes of interest into tomato has made it possible to use biotechno-logical approaches for the study of gene function. An essential prerequisite for a gene transfer system is an efficient and reliable method to regenerate plants from cells in various plant tissues. A significant amount of effort by many research groups has gone into development of an efficient regeneration system for tomato. There were several reports prior to the first reports on...

Abbreviations

Amplified fragment length polymorphism Core collection of the Brassica oleracea gene pool Cleaved amplified polymorphic sequence Derived cleaved amplified polymorphisms Fourier transform ion cyclotron resonance High-performance liquid chromatography Multinational Brassica Genome Project Minimum information about a microarray experiment National Center for Biotechnology Information S-(1 2-Propenyl)-L-cysteine sulfoxide Practical extraction and report language Random(ly) amplified polymorphic DNA...

Advanced Backcross QTL Analysis

AB-QTL was proposed by Tanksley and Nelson (1996) as a novel plant breeding scheme designed to integrate the processes of QTL discovery and variety development. Useful QTL alleles from unadapted germplasm (e.g., landraces, wild species) are identified while simultaneously being transferred to elite lines, thus streamlining the QTL identification and utilization pipeline while concurrently broadening the genetic diversity of the cultivated germplasm. In tomato, the first AB-QTL mapping project...