AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication

The pepino (Solanum muricatum) is a vegetatively propagated, domesticated native of the Andes, where it grows with wild relatives. We used AFLPs and a 1-kb sequence of the 3-methylcrotonyl-CoA carboxylase gene to study variation of 27 accessions of S. muricatum and 35 collections of 10 species of wild relatives (Solanum section Basarthrum). A total of 298 AFLP fragments and 29 DNA sequence haplotypes were detected. Cluster and principal coordinate analyses and other genetic parameters estimated from both types of markers, show that S. muricatum is closely related to the species from one of the series (Caripensia) of section Basarthrum and that >90% of the variation of the cultigen is also represented in that series. Pepino is highly diverse, either because it is not monophyletic or it has been subjected to regular introgression with wild species, or both. Although a continuous distribution of the genetic variation occurred within the cultivated species, three genetic clusters were recognized. Cluster 1 is mostly centered in Ecuador, cluster 2 in Ecuador and Peru, and cluster 3 in Colombia and Ecuador. Cluster 3 also includes all modern cultivars studied. These results and other evidence suggest that northern Ecuador/southern Colombia is the main center of pepino diversity and the center of origin. The high genetic variation of this cultigen indicates that domestication does not always produce a genetic bottleneck.     

Genetic diversity and phylogenetic relationships of the genus Lycopersicon (Tourn.) Mill. as revealed by inter-simple sequence repeat (ISSR) analysis

Inter-simple sequence repeat (ISSR) analysis was for the first time used to study the genetic diversity and phylogenetic relationships in 54 wild accessions and cultivars of the genus Lycopersicon. Analysis involved 14 ISSR primers homologous to microsatellite repeats and containing additional selective anchor nucleotides. In total, 318 ISSR fragments were amplified for the wild and cultivated tomato genomes. The interspecific polymorphism revealed with the ISSR primers was 95.6%. Species-specific ISSR fragments were detected for each tomato species. The highest number (more than 20) of species-specific fragments were obtained for L. esculentum sensu lato, although the intraspecific variation of ISSR patterns was low. UPGMA cluster analysis was used to construct a dendrogram and to estimate the genetic distances between the species of the genus Lycopersicon; between populations of L. peruvianum, L. pimpinellifolium, and L. esculentum; and between tomato cultivars. The ISSR-based phylogeny was generally consistent with Lycopersicon taxonomy based on morphological and molecular evidence, suggesting the applicability of ISSR analysis for genotyping and phylogenetic studies in tomato.     

Potassium utilization and fluxes in wild salt-tolerant relatives of the cultivated tomato

The growth of the wild tomato species Lycopersicon peruvianum (L.) Mill, and L. pennellii (Correll) D'Arcy, was compared with that of the cultivated tomato, L. esculentum Mill. cv. VE 234, under conditions of reduced K⁺ supply. Growth was impaired less in the wild than in the cultivated species. The higher efficiency of K⁺ utilization in the wild species was not associated with more efficient JC uptake from the medium. The rate of K⁺ uptake by whole plants was similar in the three species, but the rate of uptake by detached root tips was lower in the wild species. The permeability of the plasma membrane to K+ was apparently similar in root tips of the three species, but the tonoplast permeability was much lower in the wild than in the cultivated species.     

Comparative linkage map of the Solanum lycopersicoides and S. sitiens genomes and their differentiation from tomato.

The wild nightshades Solanum lycopersicoides and Solanum sitiens are closely affiliated with the tomatoes (Lycopersicon spp.). Intergeneric hybridization with cultivated tomato (Lycopersicon esculentum) is impeded by strong reproductive barriers including hybrid sterility and suppressed recombination. Conservation of genome structure between these nightshades and tomato was studied by construction of a genetic map from F2 S. sitiens x S. lycopersicoides and comparison with existing maps of tomato. Owing to self-incompatibility of the F1, two hybrid plants were crossed to obtain a population of 82 F2 individuals. Using 166 previously mapped RFLP markers and 5 restriction enzymes, 101 loci polymorphic in the S. sitiens x S. lycopersicoides population were identified. Analysis of linkage between the markers resulted in a map with 12 linkage groups covering 1192 cM and one unlinked marker. Recombination rates were similar to those observed in tomato; however, significant segregation distortion was observed for markers on 7 out of the 12 chromosomes. All chromosomes were colinear with the tomato map, except for chromosome 10, where a paracentric inversion on the long arm was detected. In this region, S. sitiens and S. lycopersicoides share the same chromosomal configuration previously reported for potato (S. tuberosum) and pepper (Capsicum), suggesting that of tomato is derived. The 10L inversion explains the lack of recombination detected among homeologous chromosomes of intergeneric hybrids in this region. On this basis, we recognize two principle genomes, designated L for the Lycopersicon spp., and S for S. lycopersicoides and S. sitiens, the first examples of structural differentiation between tomato and its cross-compatible wild relatives.     

Salinity effects on growth and carbon balance in Lycopersicon esculentum and L. pennellii

The effects of salinity on growth and carbon balance in the cultivated tomato Lycopersicon esculentum (L.) Mill. cv. VF 234 and in a wild, salt-tolerant relative, L. pennellii (Correll) D'Arcy accession Atico, were compared. The level of salinity that significantly reduced growth and affected morphology was lower for the cultivated than for the wild species.
Net CO₂ fixation, stomatal conductance and the specific activity of ribulose bisphosphate carboxylase (EC 4.1.1.39) were more decreased by salinity in the wild tomato than in the cultivated. In both species, the salinity-associated decrease in assimilation was related to a decrease in net photosynthesis and to carbon reallocation favoring heterotrophic organs.     

Evaluation of salt tolerance in cultivated and wild tomato species through in vitro shoot apex culture

The possibility of using in vitro shoot apex culture to evaluate salt tolerance of cultivated (Lycopersicon esculentum Mill.) and wild (Lycopersicon pennellii (Correll) D'Arcy) tomato species was determined and related to the response obtained by callus culture. Both apices and calluses were grown on media supplemented with 0, 35, 70, 105, 140, 175 and 210 mM NaCl, and growth and physiological traits were determined. Most apices of L. esculentum did not develop roots from low NaCl levels, whereas the apices of L. pennellii were able to develop roots at the different salt levels. This different degree of salt tolerance between L. esculentum and L. pennellii was not, however, clearly shown on the basis of the shoot growth of the plantlets. The callus response was similar to that shown by the rooting parameters, as callus growth in response to increased salinity was much greater in L. pennellii than in the tomato cultivar. K⁺decreased more and proline accumulated less with salinity in shoots of L. esculentum compared to L. pennellii, whereas the opposite response was obtained in calluses. The results obtained in this study suggest that rooting parameters are the most useful traits for rapid evaluation and screening of tomato species and segregating populations through in vitro shoot apex culture. This revised version was published online in June 2006 with corrections to the Cover Date.     

The response to NaCl of excised fully differentiated and differentiating tissues of the cultivated tomato, Lycopersicon esculentum, and its wild relatives, L. peruvianum and Solanum pennellii

The responses to NaCl of cultured leaf discs and leaflets derived from fully differentiated leaves and of shoot apices excised from the cultivated tomato Lycopersicon esculentum Mill. and its wild salt-tolerant relatives L. peruvianum (L.) Mill, and Solanum pennellii Cor were compared. The results suggest that the tolerance of the whole plant to salt depends largely on the tolerance of plant organs containing meristematic tissues rather than on tissues already differentiated. This suggestion is based on the positive correlation found between the response to NaCl of shoot apices and of the whole plant, i.e. both whole plants and apices of the wild species were more resistant to salt than those of the cultivated species. No difference was found among the species with respect to the responses of the fully differentiated parts. The ion balance (K⁺/Na⁺ and Cl⁻/Na⁺) in detached leaves and apices exposed to salt was different from the balance in the same parts while attached to the salt-treated plant. This difference may be due to the severance of the excised parts from the major sites controlling the balance of ions in the whole plant.     

Relationships, origin, and diversity of Galapagos tomatoes: implications for the conservation of natural populations

Endemic Galápagos tomatoes (Lycopersicon cheesmanii) are of great value for cultivated tomato (L. esculentum) breeding, and therefore their conservation is of significance. Although within L. cheesmanii there is heterogeneity for many traits and formal infraspecific classification is not justified, here we distinguish three forms, without taxonomic significance, of L. cheesmanii that are of interest to breeders because of their distinctive morphology and habitat preferences: L. cheesmanii 'short' (one- to two-pinnate leaves, short internodes, and coastal habitats), L. cheesmanii 'long' (one- to two-pinnate leaves, long internodes, and inland habitats), and L. cheesmanii forma minor (three- to four-pinnate leaves, short internodes, and coastal habitats). In a recent survey of tomato populations in the Galápagos Islands, we found that several populations of L. cheesmanii reported 30-50 years earlier had disappeared, mostly as a consequence of human activity. In addition, a previously unreported invasive wild red-fruited form, which we named L. esculentum 'Gal cer,' was found on the island of Santa Cruz. The total diversity (estimated with amplified fragment length polymorphisms [AFLPs]) within L. cheesmanii (H(T) = 0.051) is almost as high as that for the mainland wild species L. pimpinellifolium (H(T) = 0.072). Lycopersicon esculentum 'Gal cer,' on the other hand, has a much lower diversity (H(T) = 0.014). Comparison of AFLP fragments shared by L. esculentum 'Gal cer' with other species showed that it is closely related to weedy tomato L. esculentum var. cerasiforme and, therefore, likely of recent origin. Genetic differentiation among the three native L. cheesmanii forms is low (G(ST) = 0.235), indicating that they share a common genetic background. Nonetheless, L. cheesmanii 'short' is about twice as diverse as L. cheesmanii 'long' or L. cheesmanii f. minor. UPGMA cluster and principal components analysis distinguish four groups within Eulycopersicon: L. pimpinellifolium, cultivated L. esculentum, L. esculentum var. cerasiforme including L. esculentum 'Gal cer,' and L. cheesmanii. The geographic distance and genetic distance in the wild forms of Galápagos tomatoes were not correlated. Apart from the pressure of humans, some native L. cheesmanii populations, especially L. cheesmanii 'long,' might be displaced by invasive L. esculentum 'Gal cer' because they share a similar habitat. We did not find evidence of intercrossing of L. cheesmanii with introduced L. esculentum, but occasional hybridization that contributes to loss of genetic integrity of L. cheesmanii cannot be ruled out. Establishment of reserves of L. cheesmanii to protect this species from introduced herbivorous animals and from hybridization with L. esculentum 'Gal cer' would help to conserve L. cheesmanii. Furthermore, accessions collected by C. M. Rick and others in the 1950s-1970s and now stored in germplasm banks could be used to reinstate some extinct populations.     

Comparative genetics of hybrid incompatibility: sterility in two Solanum species crosses

The genetic basis of hybrid sterility can provide insight into the genetic and evolutionary origins of species barriers. We examine the genetics of hybrid incompatibility between two diploid plant species in the plant clade Solanum sect. Lycopersicon. Using a set of near-isogenic lines (NILs) representing the wild species Solanum pennellii (formerly Lycopersicon pennellii) in the genetic background of the cultivated tomato S. lycopersicum (formerly L. esculentum), we found that hybrid pollen and seed infertility are each based on a modest number of loci, male (pollen) and other (seed) incompatibility factors are roughly comparable in number, and seed-infertility QTL act additively or recessively. These findings are remarkably consistent with our previous analysis in a different species pair, S. lycopersicum x S. habrochaites. Data from both studies contrast strongly with data from Drosophila. Finally, QTL for pollen and seed sterility from the two Solanum studies were chromosomally colocalized, indicating a shared evolutionary history for these QTL, a nonrandom genomic distribution of loci causing sterility, and/or a proclivity of certain genes to be involved in hybrid sterility. We show that comparative mapping data can delimit the probable timing of evolution of detected QTL and discern which sterility loci likely evolved earliest among species.     

QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato and comparisons with potato.

Quantitative trait loci (QTLs) for resistance to Phytophthora infestans (late blight) were mapped in tomato. Reciprocal backcross populations derived from cultivated Lycopersicon esculentum x wild Lycopersicon hirsutum (BC-E, backcross to L. esculentum; BC-H, backcross to L. hirsutum) were phenotyped in three types of replicated disease assays (detached-leaflet, whole-plant, and field). Linkage maps were constructed for each BC population with RFLPs. Resistance QTLs were identified on all 12 tomato chromosomes using composite interval mapping. Six QTLs in BC-E (lb1a, lb2a, lb3, lb4, lb5b, and lb11b) and two QTLs in BC-H (lb5ab and lb6ab) were most consistently detected in replicated experiments or across assay methods. Lycopersicon hirsutum alleles conferred resistance at all QTLs except lb2a. Resistance QTLs coincided with QTLs for inoculum droplet dispersal on leaves, a trait in L. hirsutum that may contribute to resistance, and dispersal was mainly associated with leaf resistance. Some P. infestans resistance QTLs detected in tomato coincided with chromosomal locations of previously mapped R genes and QTLs for resistance to P. infestans in potato, suggesting functional conservation of resistance within the Solanaceae.     

Variation in Response of Wild Lycopersicon and Solanum spp. against Tomato Powdery Mildew (Oidium lycopersici)

A set of 154 accessions of nine wild Lycopersicon spp. and five accessions of three closely related Solanum spp. were tested for resistance to tomato powdery mildew ( Oidium lycopersici ). Screening revealed valuable sources of resistance, mainly among L. hirsutum, L. pennellii, L. cheesmanii, L. chilense, L. peruvianum and L. parviflorum. L. esculentum (all ssp.) and L. pimpinellifolium expressed high susceptibility to O. lycopersici inoculation. Results of variance and cluster analysis of responses to O. lycopersici coincide with recent taxonomic classification and genetic relationships within genus Lycopersicon .     

A genetic map of tomato based on BC(1) Lycopersicon esculentum x Solanum lycopersicoides reveals overall synteny but suppressed recombination between these homeologous genomes

F(1) hybrids between the cultivated tomato (Lycopersicon esculentum) and the wild nightshade Solanum lycopersicoides are male sterile and unilaterally incompatible, breeding barriers that impede further crosses to tomato. Meiosis is disrupted in 2x hybrids, with reduced chiasma formation and frequent univalents, but is normal in allotetraploid hybrids, indicating the genomes are homeologous. In this study, a partially male-fertile F(1) was backcrossed to tomato, producing the first BC(1) population suitable for genetic mapping from this cross. BC(1) plants were genotyped at marker loci to study the transmission of wild alleles and to measure rates of homeologous recombination. The pattern of segregation distortion, in favor of homozygotes on chromosomes 2 and 5 and heterozygotes on chromosomes 6 and 9, suggested linkage to a small number of loci under selection on each chromosome. Genome ratios nonetheless fit Mendelian expectations. Resulting genetic maps were essentially colinear with existing tomato maps but showed an overall reduction in recombination of approximately 27%. Recombination suppression was observed for all chromosomes except 9 and 12, affected both proximal and distal regions, and was most severe on chromosome 10 (70% reduction). Recombination between markers on the long arm of this chromosome was completely eliminated, suggesting a lack of colinearity between S. lycopersicoides and L. esculentum homeologues in this region. Results are discussed with respect to phylogenetic relationships between the species and their potential use for studies of homeologous pairing and recombination in a diploid plant genome.     

Pepino mosaic virus, a new potexvirus from pepino (Solanum muricatum)

Pepino mosaic virus (PepMV), a previously undescribed virus, was found in fields of pepino (Solanum muricatum) in the Canete valley in coastal Peru. PepMV was transmitted by inoculation of sap to 32 species from three families out of 47 species from nine families tested. It caused a yellow mosaic in young leaves of pepino and either a mild mosaic or symptomless infection in 12 wild potato species, five potato cultivars and potato clone USDA 41956 but S. stoloniferum and potato cultivars Merpata and Revolucion reacted with severe systemic necrotic symptoms. The virus was transmitted by plant contact but not by Myzus persicae. It was best propagated and assayed in Nicotiana glutinosa. Sap from infected N. glutinosa was infective after dilution to 10^-1 but not 10^-6, after 10 min at 65°C but not 70°C and after 3 months at 20°C. PepMV had filamentous particles with a normal length of 508 nm; the ends of some seemed damaged. Ultra-thin sections of infected leaves of N. glutinosa revealed many inclusions containing arrays of virus-like particles some of which were banded or whorled; small aggregates of virus-like particles were also common. The virus was purified by extracting sap from infected leaves in a solution containing 0·065 M disodium tetraborate, 0·435 M boric acid, 0·2% ascorbic acid and 0·2% sodium sulphite at pH 7·8, adding silver nitrate solution to the extract, and precipitating the virus with polyethylene glycol followed by two cycles of differential centrifugation. Particles of PepMV normally yielded two proteins with molecular weights of 26 600 and 23 200, but virus obtained from infective sap aged overnight yielded only the smaller protein suggesting that it was a product of degradation of the larger one. The virus is serologically related to two potexviruses, narcissus mosaic and cactus X and its properties are typical of the potexvirus group.     

Regeneration of intergeneric somatic hybrid plants between Lycopersicon esculentum and Solanum muricatum

Summary Mesophyll protoplasts of tomato (Lycopersicon esculentum) and pepino (Solanum muricatum) were fused by using an electrofusion method and cultured in modified MS medium supplemented with naphthaleneacetic acid and kinetin, in which only pepino and somatic hybrid protoplasts could divide. Somatic hybrid plants showing intermediate characteristics in morphology were regenerated from the calli exhibiting vigorous growth in contrast with those of pepino. The hybrid nature of these plants was confirmed by cytological observation and biochemical analyses of phosphoglucomutase isozymes and the fraction-1-protein. The regenerated somatic hybrids grew to flowering stage and set fruits.     

Susceptibility of some weed species to Pepino mosaic virus (PepMV)

The aim of our investigations was to study the susceptibility of 22 weed species to Pepino mosaic virus (PepMV). Seven plants of each species were mechanically inoculated at 4-6 leaf stage with PepMV in a vector free virological glasshouse. Inoculated plants were tested on the basis of symptoms, by DAS ELISA serological method and back inoculation. Among the 22 weed species, only some Solanum ones (S. aethiopicum, S. dulcamara, S. luteum, S. nigrum) were susceptible to PepMV infection. All of them--except S. aethiopicum--belong to Hungarian weed flora, therefore these weeds--occurring mainly in tomato ecosystems--may play important role in the epidemiology of PepMV. Other 18 weed species seemed to be resistant to PepMV, and on the basis of back inoculation not even latent infection has been observed.     

The chilling sensitivity of root ammonium influx in a cultivated and wild tomato

A chilling episode of a few hours damaged root ammonium absorption in a cultivated tomato ( Lycopersicon esculentum cv. T-5), but not in a wild congener from high altitudes ( Lycopersicon hirsutum LA1778). In the cultivar, ammonium influx was strongly temperature dependent and showed the residual effects of chilling, whereas ammonium efflux was nearly temperature invariant and showed no persistent effects. A 2 h exposure to 5 °C significantly depressed subsequent ammonium absorption at 20 °C, and about 12 h at 20 °C was required for recovery. For both the cultivated and wild species, rerooted cuttings were slightly less sensitive to chilling than seedlings. The relative inhibition (mean ± SE) of ammonium absorption before and after chilling was 58·4 ± 2·5% for the cultivated species and 29·0 ± 9·1% for the wild species. The F₁ hybrid between the species showed a relative inhibition of 52·4 ± 3·6%, suggesting that chilling sensitivity may be dominant. In a backcross of the hybrid to L. esculentum , the phenotypic distribution of the relative inhibition of ammonium absorption indicated that this trait is segregating.     

The inheritance of chilling tolerance in tomato (Lycopersicon spp.)

During the past 25 years, chilling tolerance of the cultivated (chilling-sensitive) tomato Lycopersicon esculentum and its wild, chilling-tolerant relatives L. peruvianum and L. hirsutum (and, less intensively studied, L. chilense) has been the object of several investigations. The final aim of these studies can be seen in the increase in chilling tolerance of the cultivated genotypes. In this review, we will focus on low-temperature effects on photosynthesis and the inheritance of these traits to the offspring of various breeding attempts. While crossing L. peruvianum (male symbol) to L. esculentum (female symbol) so far has brought the most detailed insight with respect to physiological questions, for practical purposes, e.g., the readily cross ability, crossing programmes with L. hirsutum as pollen donor at present seem to be a promising way to achieve higher chilling-tolerant genotypes of the cultivated tomato. This perspective is due to the progress that has been made with respect to the genetic basis of chilling tolerance of Lycopersicon spp. over the past five years.     

Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene

Phylogeographical studies are emerging as a powerful tool for understanding the population structure and evolution of wild relatives of crop species. Because of their value as genetic resources, there is great interest in exploring the distribution of variation in wild relatives of cultivated plants. In this study, we use sequence variation from the nuclear gene, fruit vacuolar invertase (Vac), to investigate the population history of Solanum pimpinellifolium. Solanum pimpinellifolium is a close relative of the cultivated tomato and has repeatedly served as a source of valuable traits for crop improvement. We sequenced the second intron of the Vac gene in 129 individuals, representing 16 populations from the northern half of Peru. Patterns of haplotype sharing among populations indicate that there is isolation by distance. However, there is no congruence between the geographical distribution of haplotypes and their genealogical relationships. Levels of outcrossing decrease towards the southernmost populations, as previously observed in an allozyme study. The geographical pattern of Vac variation supports a centre of origin in northern Peru for S. pimpinellifolium and a gradual colonization along the Pacific coast. This implies that inbreeding populations are derived from outcrossing ones and that variation present at the Vac locus predates the spread of S. pimpinellifolium. The expansion of cities and human agricultural activity in the habitat of S. pimpinellifolium currently pose a threat to the species.