Diverse Tomato Research Articles

Single seed near-infrared hyperspectral imaging in determining tomato (Solanum lycopersicum L.) seed quality in association with multivariate data analysis

Near-infrared (NIR) hyperspectral imaging was explored as a rapid and non-destructive method of investigating seed quality parameters such as seed viability and variation in tomato seed lots. The seed lots differed with year of production and variety. Four tomato varieties: Cal J, Monprecus, NCL and Chiuri from 2013, 2014 and 2015 were used in the study. The extracted NIR hyperspectral data from 975 to 2500nm were analysed by principal component analysis (PCA) and partial least squares- discriminant analysis (PLS-DA). No distinct patterns of separation between viable and non-viable tomato seeds were revealed by the PCA. Our findings showed a pattern of separation in the tomato seed lots due to production years and varieties. The PLS-DA showed the ability to predict with ∼100 percent accuracy for varietal class membership when only the seeds of a single harvest year were included in the model. The accuracy from PLS-DA on pooled samples (all seeds from all varieties) predicted varietal class membership in the range from 34 to 88 percent. High variation in the seed lots could have caused high variation in the predicted varietal class membership. The NIR regions with chemical information from CH, NH and OH had influence on the PCA and PLS-DA models. The study presents the prospects of using NIR hyperspectral imaging in varietal identification studies of tomato seeds though we recommend a thorough validation of models.

Natural Variation in Tomato Reveals Differences in the Recognition of AvrPto and AvrPtoB Effectors from Pseudomonas syringae

The Pto protein kinase from Solanum pimpinellifolium interacts with Pseudomonas syringae effectors AvrPto or AvrPtoB to activate effector-triggered immunity. The previously solved crystal structures of the AvrPto-Pto and AvrPtoB-Pto complexes revealed that Pto binds each effector through both a shared and a unique interface. Here we use natural variation in wild species of tomato to further investigate Pto recognition of these two effectors. One species, Solanum chmielewskii, was found to have many accessions that recognize only AvrPtoB. The Pto ortholog from one of these accessions was responsible for recognition of AvrPtoB and it differed from Solanum pimpinellifolium Pto by only 14 amino acids, including two in the AvrPto-specific interface, glutamate-49/glycine-51. Converting these two residues to those in Pto (histidine-49/valine-51) did not restore recognition of AvrPto. Subsequent experiments revealed that a single substitution of a histidine-to-aspartate at position 193 in Pto, which is not near the AvrPto-specific interface, was sufficient for conferring recognition of AvrPto in plant cells. The reciprocal substitution of aspartate-to-histidine-193 in Pto abolished AvrPto recognition, confirming the importance of this residue. Our results reveal new aspects about effector recognition by Pto and demonstrate the value of using natural variation to understand the interaction between resistance proteins and pathogen effectors.

Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato.

Double-digest restriction site-associated DNA sequencing (ddRAD-Seq) enables high-throughput genome-wide genotyping with next-generation sequencing technology. Consequently, this method has become popular in plant genetics and breeding. Although computational in silico prediction of restriction sites from the genome sequence is recognized as an effective approach for choosing the restriction enzymes to be used, few reports have evaluated the in silico predictions in actual experimental data. In this study, we designed and demonstrated a workflow for in silico and empirical ddRAD-Seq analysis in tomato, as follows: (i) in silico prediction of optimum restriction enzymes from the reference genome, (ii) verification of the prediction by actual ddRAD-Seq data of four restriction enzyme combinations, (iii) establishment of a computational data processing pipeline for high-confidence single nucleotide polymorphism (SNP) calling, and (iv) validation of SNP accuracy by construction of genetic linkage maps. The quality of SNPs based on de novo assembly reference of the ddRAD-Seq reads was comparable with that of SNPs obtained using the published reference genome of tomato. Comparisons of SNP calls in diverse tomato lines revealed that SNP density in the genome influenced the detectability of SNPs by ddRAD-Seq. In silico prediction prior to actual analysis contributed to optimization of the experimental conditions for ddRAD-Seq, e.g. choices of enzymes and plant materials. Following optimization, this ddRAD-Seq pipeline could help accelerate genetics, genomics, and molecular breeding in both model and non-model plants, including crops.

Genetic variation in tomato (Solanum lycopersicum L.) with special reference to quality traits

Genetic variation in tomato (<i>Solanum lycopersicum</i> L.) with special reference to quality traits

Genomic variation in tomato, from wild ancestors to contemporary breeding accessions.

BackgroundDomestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection.ResultsOur results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and “cherry tomato” are not synonymous terms. The morphologically-based term “cherry tomato” included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups.ConclusionsThis study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1444-1) contains supplementary material, which is available to authorized users.

Genetic analysis to identify good combiners for ToLCV resistance and yield components in tomato using interspecific hybridization

The interspecific hybridization for tomato leaf curl virus (ToLCV) resistance was carried out among 10 genetically diverse tomato genotypes (diversified by 50 SSR markers). Among the 10 parents, four susceptible cultivars of Solanum lycopersicum were crossed with six resistant wilds, such as S. pimpinellifolium, S. habrochaites, S. chemielewskii, S. ceraseforme, S. peruvianum and S. chilense in a line x tester mating design. All the 24 hybrids and their parents were grown in the field and glasshouse conditions to determine the general-combining abilities (GCA) and specific-combining abilities (SCA). The variances due to SCA and GCA showed both additive and nonadditive gene effects. Based on GCA estimates, EC-520061 and WIR-5032 were good general combiners while based on SCA estimates, PBC x EC-520061 and PBC x EC-521080 were best specific combiners for coefficient of infection and fruit yield per plant in both the environments. These lines could be selected and utilized in ToLCV resistance and high yield breeding programme for improving the traits.

Electrochemical tomato (Solanum lycopersicum L.) characterisation using contact probe in situ voltammetry

An in situ electrochemical contact probe methodology for characterising tomato samples is proposed. It is based on the record of the voltammetric response of antioxidant compounds when glassy carbon electrodes are inserted into the pericarp of fresh tomato specimens cut in half. The absence of pretreatment and in situ sampling avoid sample contamination and the oxidation of air-sensitive compounds thus increasing the representativity of the analytical data relative to conventional electrochemical analysis. Characteristic voltammetric responses recorded for such compounds, including rutin, chlorogenic acid, naringenin, naringenin chalcone and ascorbic acid have been obtained. A positive correlation between the (total phenolic compounds)/(ascorbic acid) ratio and peak intensity ratios has been found when analysing the voltammograms. This fact led us to differentiate between diverse tomato varieties and also tomatoes sample growth under different agronomic conditions and harvested at two ripeness stages.

Prediction of F1 progeny variation in tomato (Solanum Lycopersicum L.) from parental divergence assessed by SSR markers

Background: Although the use of heterosis is one of the most significant achievements of agriculture, the genetic mechanisms of this phenomenon still remain unclear. Development of numerous molecular tools stimulated efforts to determine the prognostic criteria for selection of best parental combinations. In result of studying the relationship between heterosis in F1 and genetic divergence of the parents, the prospects of utilizing DNA markers have not been persuasively established due to inconsistent findings. Materials and methods: Molecular-genetic data have been used to predict heterosis in F1 hybrids of tomato. Estimates of the genetic dissimilarity of parents for all pair-wise combinations of testcross (4 × 6) were performed based on patterns of 11 SSR informative markers (PIC 0.28-0.85). The general (GCA) and specific (SCA) combining ability of line, mid-parent heterosis (MPH) and high-parent heterosis (HPH) of F1 were assessed. Relationship between GD, MPH and HPH were calculated by correlation analysis. Result: The level of total SSR divergence of the parental lines was significantly associated with heterosis and SCA (sij) for fruit weight and fruit number per plant. Notably, the highest values of MPH and HPH were obtained in the most divergent pair-wise combinations. Lowest negative values of heterosis were observed in the F1 progeny from the least divergent lines. But the main group of F1 progeny demonstrates wide variation of heterosis due to SSR GD have low prognostic potential. Conclusion: Estimation of GDs may be useful for predicting promising combinations, but has limitations, since only a part of F1 heterotic advantage may be explained by the genetic divergence of its parents. Probably for understanding and manipulating heterosis the genetic divergence must be dissected to select “positive” markers, i. e. those that allow identifying the part of heterogeneity associated with the expression of heterosis in F1.

Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex.

The most diverse wild tomato species Solanum peruvianum sensu lato (s.l.) has been reclassified into four separate species: Solanum peruvianum sensu stricto (s.s.), Solanum corneliomuelleri, Solanum huaylasense, and Solanum arcanum. However, reproductive barriers among the species are incomplete and this can lead to discrepancies regarding genetic identity of germplasm. We used genotyping by sequencing (GBS) of S. peruvianum s.l., Solanum neorickii, and Solanum chmielewskii to develop tens of thousands of mapped single nucleotide polymorphisms (SNPs) to analyze genetic relationships within and among species. The data set was condensed to 14,043 SNPs with no missing data across 46 sampled plants. Origins of accessions were mapped using geographical information systems (GIS). Isolation by distance, pairwise genetic distances, and number of clusters were estimated using population genetics approaches. Isolation by distance was strongly supported, especially between interspecific pairs. Eriopersicon (S. peruvianum s.s., S. corneliomuelleri, S. huaylasense) and Arcanum (S. arcanum, S. neorickii, S. chmielewskii) species groups were genetically distinct, except for S. huaylasense which showed 50% membership proportions in each group. Solanum peruvianum and S. corneliomuelleri were not significantly differentiated from each other. Many thousands of SNP markers were identified that could potentially be used to distinguish pairs of species, including S. peruvianum versus S. corneliomuelleri, if they are verified on larger numbers of samples. Diagnostic markers will be valuable for delimiting morphologically similar and interfertile species in germplasm management. Approximately 12% of the SNPs rejected a genome-wide test of selective neutrality based on differentiation among species of S. peruvianum s.l. These are candidates for more comprehensive studies of microevolutionary processes within this species complex.

Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging

Root systems show considerable plasticity in their morphology and physiology in response to variability within their environment. Root elongation below a water-table was expected to slow due to hypoxia, whilst roots above the waterlogged zone were expected to compensate by increasing elongation rates. Tomato plants (Solanum lycopersicum L.) were grown in peat in root chambers (300 × 215 × 6 mm) with a transparent front. Root chambers were maintained in flatbed scanners tilted at 30° to vertical and scanned every 3 h before, during and after waterlogging the lower layer for 24 h or 5 days. Root elongation rates were calculated from the displacement of randomly selected root tips between successive scans. Oxygen content was determined in the waterlogged layer and plant and root parameters were determined at cessation of the experiment. Root elongation rates decreased rapidly when waterlogged. Growth rates of the waterlogged roots decreased, while growth rates of roots above the waterlogged zone increased. In 24 h waterlogged roots new lateral root growth occurred in the lower layer of the root chamber when water was drained while after 5 day waterlogging new root growth had to be initiated from roots above the waterlogged zone. Plants increased growth rates in roots above the waterlogged zone probably as compensation for the suboptimal conditions in the waterlogged zone which eventually led to roots dying.

Lycopene isomers in fresh and processed tomato products: Correlations with instrumental color measurements by digital image analysis and spectroradiometry

Tomatoes (Solanum lycopersicum L.) are food staples that contain high levels of lycopene (LYC), a red carotenoid thought to provide health benefits. Previous studies indicate that instrumental color measurements can be harnessed to estimate carotenoid levels in a rapid and non-destructive fashion, which offers important analytical advantages. In this investigation we have assessed the different LYC isomer contents by HPLC and the color of diverse tomato genotypes and tomato derived-products by SPR and DIA with four main purposes: 1) to compare the levels of LYC isomers in processed vs fresh tomato products, 2) to evaluate the validity of DIA and SPR to ascertain the color of these products, 3) to compare the ability of both instrumental methodologies to discriminate between the two different groups of samples, and 4) to compare the utility of both methodologies for estimating LYC levels. The results indicated that the parameters obtained by SPR and DIA were significantly correlated (p<0.05) and that the higher regression coefficients were obtained for L*, C*ab and a*. This observation indicates that the DIA is appropriate to evaluate the color of tomato. It was also noticed that, overall, SPR led to better discriminations between samples considering the PCA data (97%).

Multiple Divergent ITS1 Copies Were Identified in Single Tomato Genome Using DGGE Analysis

The intra-genomic variation in the internal transcribed spacer (ITS) region has led to misleading conclusions in the evolutionary analysis of plants; understanding this variation is critical for correct evolutionary analysis based on ITS sequences. To reveal the ITS variation in tomato, entire copies of ITS1 sequences within tomato species were separated using denaturing gradient gel electrophoresis (DGGE) and DNA sequence analysis. ITS1 copies varied significantly in sequence composition, but not in sequence length within the same tomato cultivar. DNA sequence similarity of the ITS1 copies was 77–100 %. Moreover, AT and GC contents in ITS1 copies from each tomato cultivar were significantly different, ranging from 50.4 to 64.3 % for GC and from 35.7 to 49.6 % for AT. However, the length variation of ITS1 was insignificant, ranging from 279 to 282 bp. Multiple copies of divergent ITS1 present in the tomato genome indicate that some copies may be paralogues. In conclusion, DGGE technique is a reliable and novel approach to reveal the entire ITS copy variation and the possible evolutionary relationship of tomato.

Magnitude of Genotype × Environment Interactions Affecting Tomato Fruit Quality

There is a growing interest by consumers to purchase fresh tomatoes with improved quality traits including lycopene, total soluble solids (TSS), vitamin C, and total titratable acid (TTA) content. As a result, there are considerable efforts by tomato breeders to improve tomato for these traits. However, suitable varieties developed for one location may not perform the same in different locations. This causes a problem for plant breeders because it is too labor-intensive to develop varieties for each specific location. The objective of this study was to determine the extent of genotype × environment (G×E) interaction that influences tomato fruit quality. To achieve this objective, we grew a set of 42 diverse tomato genotypes with different fruit shapes in replicated trials in three locations: North Carolina, New York, and Ohio. Fruits were harvested at the red ripe stage and analyzed for lycopene, TSS, vitamin C, and TTA. Analysis of variance (ANOVA) revealed that there were significant differences (P &lt; 0.05) among tomato genotypes, locations, and their interaction. Further analysis of quality traits from individual locations revealed that there was as much as 211% change in performance of some genotypes in a certain location compared with the average performance of a genotype. Lycopene was found to be most influenced by the environment, whereas TTA was the least influenced. This was in agreement with heritability estimates observed in the study for these quality traits, because heritability estimate for lycopene was 16%, whereas that for TTA was 87%. The extent of G×E interaction found for the fruit quality traits in the tomato varieties included in this study may be useful in identifying optimal locations for future field trials by tomato breeders aiming to improve tomato fruit quality.

Effects of Salinity Stress on Carotenoids, Anthocyanins, and Color of Diverse Tomato Genotypes

One nonanthocyanin-accumulating (Ailsa Craig) and three anthocyanin-accumulating tomato genotypes (Anthocyanin fruit type, Atroviolaceum, and Sun Black) were analyzed to assess differences in their carotenoid and anthocyanin levels and color and to evaluate the effects of nutrient solutions with different salt concentrations on these parameters. The carotenoid content of control Atroviolaceum tomatoes was ca. 2-2.5-fold higher relative to the other two types, and the color of its puree could be visually distinguished from those of other genotypes. Salinity stress led in some cases to a 2-3-fold increase in the lycopene content. Saline treatment increased the accumulation of total anthocyanins in fruits of Sun Black (2-fold increase), while it reduced it in fruits of Anthocyanin (10-fold decrease). In general, the treatment increased the differences in color of different purees. These results indicate that salinity stress can lead to similar or higher increases in tomato carotenoids than those achieved by genetic engineering. In addition, these changes were accompanied by visually discernible color differences in tomato products. Our findings show the considerable potential of exploiting saline soils to obtain tomatoes with higher levels of secondary metabolites like carotenoids and anthocyanins.

Single Laboratory Validation of a Microsatellite Marker-Based Method in Tomato Variety Identification

The objective of this study was to develop a systematic and flexible method for assembling multiplex simple sequence repeat marker panels for high-throughput genome analysis in the tomato, Solanum lycopersicum, for varietal identification and to demonstrate the technical viability of these genetic markers for use in the enforcement of U.S. Department of Agriculture marketing order-based identity preservation programs. GeneMapper, a semiautomated software tool, was used for designing multiplex panels, allele identification, and polymorphism pattern evaluation of diverse tomato cultivars. Semiautomated genotyping was performed on a set of 12 microsatellite markers providing genome-wide coverage of the tomato chromosomes. Microsatellites were detected with fluorescently labeled primers grouped into five multiplex panels, and each primer pair was assessed in replicated trials for reliability of allele size estimates. Allele sizes for each locus were compared, and a database for 34 tomato varieties was developed. The microsatellite marker set identified distinct allelic peaks and unique genetic fingerprints for each of the studied tomato varieties. A "blind testing" exercise with UglyRipe and Vintage Ripe tomato varieties, using the above set of markers and database, further established the usefulness of these microsatellite markers for tomato commodity marketing order enforcement.

INDUCED MUTAGENESIS AND NATURAL GENETIC VARIATION IN TOMATO 'MICRO-TOM'

INDUCED MUTAGENESIS AND NATURAL GENETIC VARIATION IN TOMATO 'MICRO-TOM'

A correlation network approach to metabolic data analysis for tomato fruits

Network analysis of correlations between abundances of metabolites across tomato genotypes can help in unraveling the biological basis of organoleptic variation in tomato. We illustrate how to construct and interpret simple correlations networks using metabolic data collected on a diverse set of tomato genotypes. Various types of correlations are calculated and displayed in the form of networks. Interpretations on the basis of network analyses are compared to interpretations following principal components analysis.

Metabolomics and trait development in crops

Genetic modification to elicit trait improvements in crops can be pursued through conventional breeding, irradiation, chemical mutagenesis and modern biotechnological approaches. These latter approaches have recently expanded to include both the use of RNAi silencing and the modification of genes encoding regulatory proteins. The emergence of these new biotechnological options coincides with continuing technical and informatics advances in the ‘omics sciences. The purpose of the ‘‘Metabolomics and Trait Development’’ focus of this journal issue is to discuss how metabolomics can integrate with modern biotechnological strategies, as well as with conventional approaches, to drive trait enhancements in major crops. An introductory review by Harrigan and colleagues considers the potential of metabolomics in assessing natural variation and metabolic diversity in plants. Two original research articles then follow that highlight applications of metabolic profiling in characterizing metabolic variation in tomato during growth and development (Mounet et al.) and exposure to drought (Semel et al.). A third research article describes methodology for assessing sub-cellular compartmentation in the soy metabolome (Benkeblia et al.). Subsequent articles consider more directly the value of metabolomics in studies of plants modified through modern biotechnology. This is first illustrated by research on the effects of manipulating tomato metabolism through expression of a moss-derived sodium pumping ATPase. The metabolic and phenotypic changes induced by manipulating ion homeostasis are difficult to predict yet a metabolomics program yielded information that can now guide more detailed mechanism-of-action studies (Jacobs et al.). Hypotheses-driven or ‘‘targeted’’ profiling can also be of immense value in evaluating metabolic changes associated with manipulation of a specific metabolic pathway. Wakasa and colleagues, for example, demonstrate that metabolome changes associated with deregulation of tryptophan synthesis through expression of mutant forms of anthranilate synthase in rice and other crops are quite minimal. A fundamental concern regarding the use of ‘‘nontargeted’’ metabolic profiling approaches in compositional assessments of crops centers on the fact that the number of acquired data points can greatly exceed the number of experimental samples in a typical study. Indeed, Enot and colleagues emphasize that few studies prescribe ‘‘distance metrics’’ for determining whether there are, in fact, biologically meaningful differences in the metabolomes of different test materials. They describe a hierarchical approach that may provide greater statistical rigor to profiling experiments; this is expanded upon in the follow-up paper by Enot and Draper which posits the value of machine learning in studies using high content data. RNAi silencing is proving to be an important strategy for effecting loss-of-function mutations. Tang and colleagues present an excellent overview of the technology involved and provide examples of its applications. This article also serves as an introduction to three reviews that describe RNAi silencing approaches, and other transgenic strategies, to the manipulation of a number of important biochemical pathways. These include the pharmaceutically significant benzlyisoquinoline pathway in poppy (Larkin and Harrigan), cyanogenic glucoside synthesis in a range of plants (Morant et al.) and flavonoid synthesis in tomato (Bovy et al.). A role for targeted metabolomics in assessing G. G. Harrigan (&) Product Safety Center, Monsanto Company, 800 North Lindbergh Blvd., St. Louis, MO 63167, USA e-mail: george.g.harrigan@monsanto.com

Effect of Cooking Processes on the Contents of Two Bioactive Carotenoids in Solanum lycopersicum Tomatoes and Physalis ixocarpa and Physalis philadelphica Tomatillos

Calculation of the HPLC chromatographic retention times of different carotenoids supported our improved chromatographic separation of beta-carotene and lutein in four tomatoes and two tomatillo varieties in fresh form and after three different cooking procedures: pot boiling, cooking in a pressure cooker and microwaving. A good separation was achieved experimentally using an Ultrasphere ODS column and gradient elution with an acetonitrile-tetrahydrofuran-water mobile phase. It was shown that diverse tomato species contained different amounts of beta-carotene (6-400 microg/100 mg) and lutein (2-30 microg/100 mg). The concentration in fresh samples was higher than in cooked tomatoes. The beta-carotene content in fresh tomatillo varied between 2 and 20 microg/100 mg. Microwaving caused partial destruction of the beta-carotene and lutein in tomatillos.

Morphological variation in tomato: a comprehensive study of quantitative trait loci controlling fruit shape and development

Variation in fruit morphology is a prevalent characteristic among cultivated tomato. The genetic and developmental mechanisms underlying similarities and differences in shape between the fruit of two elongated tomato varieties were investigated. Fruit from two F2 populations constructed from either Solanum lycopersicum cv. Howard German or cv. Banana Legs crossed with S. pimpinellifolium accession LA1589, and one BC1 population constructed with S. lycopersicum Howard German as the recurrent parent, were analysed for shape by using a new software program Tomato Analyzer. Quantitative trait loci (QTLs) controlling 15 individual shape attributes were mapped by both single and multitrait composite interval mapping in each population. In addition, principal components analysis and canonical discriminant analysis were conducted on these shape attributes to determine the greatest sources of variation among and between the populations. Individual principal components and canonical variates were subjected to QTL analysis to map regions of the genome influencing fruit shape in the cultivars. Common and unique regions, as well as previously known and novel QTLs, underlying fruit morphology in tomato were identified. Four major loci were found to control multiple fruit shape traits, principal components, and canonical variates in the populations. In addition, QTLs associated with the principal components better revealed regions of the genome that varied among populations than did the QTL associated with canonical variates. The QTL identified can be compared across additional populations of tomato and other fruit-bearing crop species.