Ecological and evolutionary genomics in the wild tomatoes (Solanum sect. Lycopersicon)

A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L

Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships. We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size. Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits. We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.

A catalogue of recombination coldspots in interspecific tomato hybrids

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.

A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought

Introduction

Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources.

Methods

In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads.

Results

The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production.

Discussion

Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.

The balance of survival: Comparative drought response in wild and domesticated tomatoes

Plants have the ability to undergo reversible behavioral, morphological, or physiological changes in response to environmental conditions. This plasticity enables plants to cope with uncertain environmental conditions, such as drought. A primary plastic trait is the rate of stomatal response to changes in ambient conditions, which determines the amount of water lost via transpiration, as well as levels of CO2 absorption, growth, and productivity. Here, we examined the differences between domesticated (S. lycopersicum cv. M82) and wild tomato (S. pennellii) species and their responses to drought stress. The plants were grown in pots in a functional phenotyping platform (FPP) in a semi-controlled environment greenhouse. We found that the domesticated tomato had a higher transpiration rate (E) and higher stomatal conductance (gs). The domesticated tomato also had greater biomass and greater leaf area under drought conditions, as compared to the wild tomato. Despite the domesticated tomato's higher E and higher gs, there was no difference between the photosynthetic rates (An) of the two lines. Moreover, the wild tomato had a higher maximum rate of rubisco activity (Vcmax), which might explain its greater leaf level and whole canopy water-use efficiency. The domesticated tomato's higher E and greater leaf area led to its earlier exposure to drought stress, as compared to the wild tomato, which maintained higher levels of soil water, enabling it to maintain steady rates of whole-canopy stomatal conductance (gsc) for extended periods. The wild tomato was also more sensitive to soil water availability and lowered its maximum transpiration rate (Emax) at a higher soil-water-content (SWC) level compared to the domesticated species. Our results suggest that the domestication of tomatoes favored morphological/anatomical performance traits over physiological efficiency.

Diversity of tomato leaf form provides novel insights into breeding

Tomato (Solanum lycopersicum L.) is cultivated widely globally. The crop exhibits tremendous morphological variations because of its long breeding history. Apart from the commercial tomato varieties, wild species and heirlooms are grown in certain regions of the world. Since the fruit constitutes the edible part, much of the agronomical research is focused on it. However, recent studies have indicated that leaf morphology influences fruit quality. As leaves are specialized photosynthetic organs and the vascular systems transport the photosynthetic products to sink organs, the architectural characteristics of the leaves have a strong influence on the final fruit quality. Therefore, comprehensive research focusing on both the fruit and leaf morphology is required for further tomato breeding. This review summarizes an overview of knowledge of the basic tomato leaf development, morphological diversification, and molecular mechanisms behind them and emphasizes its importance in breeding. Finally, we discuss how these findings and knowledge can be applied to future tomato breeding.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Auxin-driven ecophysiological diversification of leaves in domesticated tomato

Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the parenchyma, whereas homobaric leaves do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. The tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here, we identify the obv gene and the causative mutation, a nonsynonymous amino acid change that disrupts a C2H2 zinc finger motif in a putative transcription factor. This mutation exists as a polymorphism in the natural range of wild tomatoes but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The obv mutant displays reduced vein density, leaf hydraulic conductance and photosynthetic assimilation rate. We show that these and other pleiotropic effects on plant development, including changes in leaf insertion angle, leaf margin serration, minor vein density, and fruit shape, are controlled by OBV via changes in auxin signaling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results in defective BSE development, revealing an additional component of a genetic module controlling aspects of leaf development important for ecological adaptation and subject to breeding selection.

Distribution and Climatic Adaptation of Wild Tomato (Solanum lycopersicum L.) Populations in Mexico

Tomato (Solanum lycopersicum L.) is a vegetable with worldwide importance. Its wild or close related species are reservoirs of genes with potential use for the generation of varieties tolerant or resistant to specific biotic and abiotic factors. The objective was to determine the geographic distribution, ecological descriptors, and patterns of diversity and adaptation of 1296 accessions of native tomato from Mexico. An environmental information system was created with 21 climatic variables with a 1 km² spatial resolution. Using multivariate techniques (Principal Component Analysis, PCA; Cluster Analysis, CA) and Geographic Information Systems (GIS), the most relevant variables for accession distribution were identified, as well as the groups formed according to the environmental similarity among these. PCA determined that with the first three PCs (Principal Components), it is possible to explain 84.1% of the total variation. The most relevant information corresponded to seasonal variables of temperature and precipitation. CA revealed five statistically significant clusters. Ecological descriptors were determined and described by classifying accessions in Physiographic Provinces. Temperate climates were the most frequent among tomato accessions. Finally, the potential distribution was determined with the Maxent model with 10 replicates by cross-validation, identifying areas with a high probability of tomato presence. These results constitute a reliable source of useful information for planning accession sites collection and identifying accessions that are vulnerable or susceptible to conservation programs.

Dynamics of Fertility-Related Traits in Tomato Landraces under Mild and Severe Heat Stress

Studies on the reproductive dynamics under heat stress are crucial to breed more tolerant cultivars. In tomato, cultivars, breeding lines, and wild species have been evaluated for their response to heat stress. Here, we addressed the study to a panel of selected landraces representing traditional genotypes that usually show high adaptation to local environments. In two experiments, spaced by 12 years, we set-up an identical experimental design with plants transplanted at two different dates to expose the second field to thermic stress with natural fluctuations. Such a strategy resulted in both a mild and severe stress in the two years. The landraces showed wide variation for both vegetative and reproductive traits; all traits were affected by heat, mostly with a significant Genotype*Environment interaction. A high broad-sense heritability was estimated for plant height, stigma position, pollen viability, and fruit weight. Low heritability estimates were found for the number of flowers, fruit set, and yield. Despite the interaction, traits recorded under control and heat conditions were positively correlated. Multivariate analysis located the genotypes in a topography that was stable under all conditions, except under the harshest temperatures. The study revealed that landraces present a wide variability for the response of reproductive traits to thermic challenges and that such a variation could be useful to dissect the traits with higher heritability and identify quantitative trait loci for breeding more resilient varieties.

Inferring genome-wide correlations of mutation fitness effects between populations

The effect of a mutation on fitness may differ between populations depending on environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in mutation fitness effects, we developed a novel concept called a joint distribution of fitness effects (DFE) between populations. We then proposed a new statistic w to measure the DFE correlation between populations. Using simulation, we showed that inferring the DFE correlation from the joint allele frequency spectrum is statistically precise and robust. Using population genomic data, we inferred DFE correlations of populations in humans, Drosophila melanogaster, and wild tomatoes. In these species, we found that the overall correlation of the joint DFE was inversely related to genetic differentiation. In humans and D. melanogaster, deleterious mutations had a lower DFE correlation than tolerated mutations, indicating a complex joint DFE. Altogether, the DFE correlation can be reliably inferred, and it offers extensive insight into the genetics of population divergence.

Biosystematic studies on the status of Solanum chilense

PREMISE

Common taxonomic practices, which condition species' descriptions on diagnostic morphological traits, may systematically lump outcrossing species and unduly split selfing species. Specifically, higher effective population sizes and genetic diversity of obligate outcrossers are expected to result less reliable phenotypic diagnoses. Wild tomatoes, members of Solanum sect. Lycopersicum, are commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although the section experienced significant early work, which continues presently, the taxonomic status of many wild species has undergone a number of significant revisions and remains uncertain. Species in this section vary in their breeding systems, notably the expression of self-incompatibility, which determines individual propensity for outcrossing METHODS: Here, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced-representation sequencing (RAD-seq), a range of phylogenetic and population genetic analyses, as well as analyses of crossing and morphological data.

RESULTS

Overall, each of our analyses provides a considerable weight of evidence that the Pacific coastal populations and Andean inland populations of the currently described Solanum chilense represent separately evolving populations, and conceal at least one undescribed cryptic species.

CONCLUSIONS

Despite its vast economic importance, Solanum sect. Lycopersicon still exhibits considerable taxonomic instability. A pattern of under-recognition of outcrossing species may be common, not only in tomatoes, but across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference.

De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme, by long-read sequencing

The ancestral tomato species are known to possess genes that are valuable for improving traits in breeding. Here, we aimed to construct high-quality de novo genome assemblies of Solanum pimpinellifolium ‘LA1670’ and S. lycopersicum var. cerasiforme ‘LA1673’, originating from Peru. The Pacific Biosciences (PacBio) long-read sequences with 110× and 104× coverages were assembled and polished to generate 244 and 202 contigs spanning 808.8 Mbp for ‘LA1670’ and 804.5 Mbp for ‘LA1673’, respectively. After chromosome-level scaffolding with reference guiding, 14 scaffold sequences corresponding to 12 tomato chromosomes and 2 unassigned sequences were constructed. High-quality genome assemblies were confirmed using the Benchmarking Universal Single-Copy Orthologs and long terminal repeat assembly index. The protein-coding sequences were then predicted, and their transcriptomes were confirmed. The de novo assembled genomes of S. pimpinellifolium and S. lycopersicum var. cerasiforme were predicted to have 71,945 and 75,230 protein-coding genes, including 29,629 and 29,185 non-redundant genes, respectively, as supported by the transcriptome analysis results. The chromosome-level genome assemblies coupled with transcriptome data sets of the two accessions would be valuable for gaining insights into tomato domestication and understanding genome-scale breeding.

Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance

Natural plant populations encounter strong pathogen pressure and defence-associated genes are known to be under selection dependent on the pressure by the pathogens. Here, we use populations of the wild tomato Solanum chilense to investigate natural resistance against Cladosporium fulvum, a well-known ascomycete pathogen of domesticated tomatoes. Host populations used are from distinct geographical origins and share a defined evolutionary history. We show that distinct populations of S. chilense differ in resistance against the pathogen. Screening for major resistance gene-mediated pathogen recognition throughout the whole species showed clear geographical differences between populations and complete loss of pathogen recognition in the south of the species range. In addition, we observed high complexity in a homologues of Cladosporium resistance (Hcr) locus, underlying the recognition of C. fulvum, in central and northern populations. Our findings show that major gene-mediated recognition specificity is diverse in a natural plant-pathosystem. We place major gene resistance in a geographical context that also defined the evolutionary history of that species. Data suggest that the underlying loci are more complex than previously anticipated, with small-scale gene recombination being possibly responsible for maintaining balanced polymorphisms in the populations that experience pathogen pressure.

The climatic association of population divergence and future extinction risk of Solanum pimpinellifolium

Under intraspecific differentiation driven by differential climatic adaptation, it may be expected that intraspecific genetic groups occur at distinct environments. Populations occupying different niches may therefore differ in their ability to cope with climate change. Here, we addressed this hypothesis with a wild tomato, Solanum pimpinellifolium. This species is distributed from the west side of Andes to the coastal region in Peru and Ecuador and occupies a wide environmental diversity. This environmental diversity is related to the genetic structure of the species providing an ideal material to investigate the isolation by environment hypothesis. While previous hypothesis stated that S. pimpinellifolium originated from northern Peru and migrated northwards and southwards, our results support that S. pimpinellifolium originated from Ecuador and expanded to northern and southern Peru, and during this process, the niche space of S. pimpinellifolium became more associated with cold and drought. We further predicted its fate under anthropogenic climate change. According to our predictions, the northern group will maintain its current extent or even expand to the entire western region of Ecuador. In contrast, we predicted low habitat suitability for the southern group which could potentially lead to the shrinkage of its distribution. In conclusion, we revealed the distinct fates among the differentiated populations driven by environment under global warming conditions.

Assessing biological factors affecting postspeciation introgression

An increasing number of phylogenomic studies have documented a clear “footprint” of postspeciation introgression among closely related species. Nonetheless, systematic genome‐wide studies of factors that determine the likelihood of introgression remain rare. Here, we propose an a priori hypothesis‐testing framework that uses introgression statistics—including a new metric of estimated introgression, D_p—to evaluate general patterns of introgression prevalence and direction across multiple closely related species. We demonstrate this approach using whole genome sequences from 32 lineages in 11 wild tomato species to assess the effect of three factors on introgression—genetic relatedness, geographical proximity, and mating system differences—based on multiple trios within the “ABBA–BABA” test. Our analyses suggest each factor affects the prevalence of introgression, although our power to detect these is limited by the number of comparisons currently available. We find that of 14 species pairs with geographically “proximate” versus “distant” population comparisons, 13 showed evidence of introgression; in 10 of these cases, this was more prevalent between geographically closer populations. We also find modest evidence that introgression declines with increasing genetic divergence between lineages, is more prevalent between lineages that share the same mating system, and—when it does occur between mating systems—tends to involve gene flow from more inbreeding to more outbreeding lineages. Although our analysis indicates that recent postspeciation introgression is frequent in this group—detected in 15 of 17 tested trios—estimated levels of genetic exchange are modest (0.2–2.5% of the genome), so the relative importance of hybridization in shaping the evolutionary trajectories of these species could be limited. Regardless, similar clade‐wide analyses of genomic introgression would be valuable for disentangling the major ecological, reproductive, and historical determinants of postspeciation gene flow, and for assessing the relative contribution of introgression as a source of genetic variation.

Bactericera cockerelli resistance in the wild tomato Solanum habrochaites is polygenic and influenced by the presence of Candidatus Liberibacter solanacearum

The tomato-potato psyllid (TPP), Bactericera cockerelli, is a vector for the phloem-limited bacterium Candidatus Liberibacter solanacearum (Lso), the causative agent of economically important diseases including tomato vein-greening and potato zebra chip. Here, we screened 11 wild tomato relatives for TPP resistance as potential resources for tomato (Solanum lycopersicum) cultivar development. Six accessions with strong TPP resistance (survival <10%) were identified within S. habrochaites, S. pennelli, S. huaylasense, S. chmielewskii, S. corneliomulleri, and S. galapagense. Two S. pennelli and S. corneliomulleri accessions also showed resistance to Lso. We evaluated recombinant inbred lines (RILs) carrying resistance from S. habrochaites accession LA1777 in the S. lycopersicum background and identified major quantitative trait loci (QTLs) responsible for adult TPP mortality and fecundity in several RILs carrying insertions in different chromosomes, indicating the polygenic nature of these traits. Analysis of a major resistance QTL in RIL LA3952 on chromosome 8 revealed that the presence of Lso is required to increase adult TPP mortality. By contrast, the reduced TPP oviposition trait in LA3952 is independent of Lso. Therefore, resistance traits are available in wild-tomato species, although their complex inheritance and modes of action require further characterisation to optimise their utilisation for tomato improvement.

Assessment of Genetic Differentiation and Linkage Disequilibrium in Solanum pimpinellifolium Using Genome-Wide High-Density SNP Markers

To mine new favorable alleles for tomato breeding, we investigated the feasibility of utilizing Solanum pimpinellifolium as a diverse panel of genome-wide association study through the restriction site-associated DNA sequencing technique. Previous attempts to conduct genome-wide association studies using S. pimpinellifolium were impeded by an inability to correct for population stratification and by lack of high-density markers to address the issue of rapid linkage disequilibrium decay. In the current study, a set of 24,330 SNPs was identified using 99 S. pimpinellifolium accessions from the Tomato Genetic Resource Center. Approximately 84% of PstI site-associated DNA sequencing regions were located in the euchromatic regions, resulting in the tagging of most SNPs on or near genes. Our genotypic data suggested that S. pimpinellifolium were divided into three single-ancestry subpopulations and four mixed-ancestry subpopulations. Additionally, our SNP genotypic data consistently confirmed the genetic differentiation, achieving a relatively reliable correction of population stratification. Previous studies utilized the 8K tomato SNP array, SolCAP, to investigate the genetic variation of S. pimpinellifolium and we performed a meta-analysis of these genotypes. The result suggested SolCAP array was less appropriate to profile the genetic differentiation of S. pimpinellifolium when more accessions were involved because the samples belonging to the same accession demonstrated different genome patterns. Moreover, as expected, rapid linkage disequilibrium decay was observed in S. pimpinellifolium, especially in euchromatic regions. Approximately two-thirds of the flanking SNP markers did not display linkage disequilibrium based on r² = 0.1. However, the 18-Kb linkage disequilibrium decay indeed reveals the potential of single-gene resolution in GWAS when markers are saturated.

Tomato stigma exsertion induced by high temperature is associated with the jasmonate signalling pathway

High temperature (HT) is becoming an increasingly serious factor in limiting crop production with global climate change. During hot seasons, owing to prevailing HT, cultivated tomatoes are prone to exhibiting stigma exsertion, which hampers pollination and causes fruit set failure. However, the underlying regulatory mechanisms of the HT-induced stigma exsertion remain largely unknown. Here, we demonstrate that stigma exsertion induced by HT in cultivated tomato is caused by more seriously shortened stamens than pistils, which is different from the stigma exsertion observed in wild tomato species. Under the HT condition, the different responses of pectin, sugar, expansin, and cyclin cause cell wall remodelling and differentially localized cell division and selective cell enlargement, which further determine the lengths of stamens and pistils. In addition, auxin and jasmonate (JA) are implicated in regulating cell division and cell expansion in stamens and pistils, and exogenous JA instead of auxin treatment can effectively rescue tomato stigma exsertion through regulating the JA/COI1 signalling pathway. Our findings provide a better understanding of stigma exsertions under the HT condition in tomato and uncover a new function of JA in improving plant abiotic stress tolerance.

Regulation of Root Angle and Gravitropism

Regulation of plant root angle is critical for obtaining nutrients and water and is an important trait for plant breeding. A plant’s final, long-term root angle is the net result of a complex series of decisions made by a root tip in response to changes in nutrient availability, impediments, the gravity vector and other stimuli. When a root tip is displaced from the gravity vector, the short-term process of gravitropism results in rapid reorientation of the root toward the vertical. Here, we explore both short- and long-term regulation of root growth angle, using natural variation in tomato to identify shared and separate genetic features of the two responses. Mapping of expression quantitative trait loci mapping and leveraging natural variation between and within species including Arabidopsis suggest a role for PURPLE ACID PHOSPHATASE 27 and CELL DIVISION CYCLE 73 in determining root angle.

The ratio of trichomes to stomata is associated with water use efficiency in Solanum lycopersicum (tomato)

Trichomes are specialised structures that originate from the aerial epidermis of plants, and play key roles in the interaction between the plant and the environment. In this study we investigated the trichome phenotypes of four lines selected from the Solanum lycopersicum × Solanum pennellii introgression line (IL) population for differences in trichome density, and their impact on plant performance under water-deficit conditions. We performed comparative analyses at morphological and photosynthetic levels of plants grown under well-watered (WW) and also under water-deficit (WD) conditions in the field. Under WD conditions, we observed higher trichome density in ILs 11-3 and 4-1, and lower stomatal size in IL 4-1 compared with plants grown under WW conditions. The intrinsic water use efficiency (WUEi ) was higher under WD conditions in IL 11-3, and the plant-level water use efficiency (WUEb ) was also higher in IL 11-3 and in M82 for WD plants. The ratio of trichomes to stomata (T/S) was positively correlated with WUEi and WUEb , indicating an important role for both trichomes and stomata in drought tolerance in tomato, and offering a promising way to select for improved water use efficiency of major crops.

Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits

Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8 M and 56.4 M of 30-150 bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC.

Genetic variation among Saudi tomato (Solanum lycopersicum L.) landraces studied using SDS-PAGE and SRAP markers

Genetic diversity among seven Saudi tomato landraces collected from different regions of the country was assessed using SDS-PAGE and molecular (sequence-related amplified polymorphism- SRAP) markers. A total of 19 alternative protein bands with different mobility rates were identified within a molecular weight range of 9.584–225 KDa, with 53% polymorphism. Specific protein bands were observed in the “Hail 548” and “Qatif 565” landraces. Genetic similarity based on Jaccard’s coefficient ranged from 0.53 to 1.00, with an average of 0.72. For molecular evaluation, 143 amplicons (fragments) were generated using 27 SRAP primer pair combinations, of which 88 were polymorphic across all the landraces. The PIC values ranged from 0.46 to 0.90, with an average of 0.76. All landraces showed an average of 0.66 similarity coefficient value. The UPGMA dendrogram supported by principal coordinate analysis (PCoA) revealed clusters of the landraces that almost corresponded to their geographical origin. Thus, seed storage protein profiling based on SDS-PAGE and SRAP markers can efficiently be used to assess genetic variability among tomato germplasms. The information obtained in the analysis will be of great interest in the management of ex situ collections for utilization in breeding programs or for direct use in quality markets.

Resistance to Tomato Yellow Leaf Curl Virus in Tomato Germplasm

Tomato yellow leaf curl virus (TYLCV) is a virus species causing epidemics in tomato (Solanum lycopersicum) worldwide. Many efforts have been focused on identification of resistance sources by screening wild tomato species. In many cases, the accession numbers were either not provided in publications or not provided in a consistent manner, which led to redundant screenings. In the current study, we summarized efforts on the screenings of wild tomato species for TYLCV resistance from various publications. In addition, we screened 708 accessions from 13 wild tomato species using different inoculation assays (i.e., whitefly natural infection and Agrobacterium-mediated inoculation) from which 138 accessions exhibited no tomato yellow leaf curl disease (TYLCD) symptoms. These symptomless accessions include 14 accessions from S. arcanum, 43 from S. chilense, 1 from S. chmielewskii, 28 from S. corneliomulleri, 5 from S. habrochaites, 4 from S. huaylasense, 2 from S. neorickii, 1 from S. pennellii, 39 from S. peruvianum, and 1 from S. pimpinellifolium. Most of the screened S. chilense accessions remained symptomless. Many symptomless accessions were also identified in S. arcanum, S. corneliomulleri, and S. peruvianum. A large number of S. pimpinellifolium accessions were screened. However, almost all of the tested accessions showed TYLCD symptoms. Further, we studied allelic variation of the Ty-1/Ty-3 gene in few S. chilense accessions by applying virus-induced gene silencing and allele mining, leading to identification of a number of allele-specific polymorphisms. Taken together, we present a comprehensive overview on TYLCV resistance and susceptibility in wild tomato germplasm, and demonstrate how to study allelic variants of the cloned Ty-genes in TYLCV-resistant accessions.

Exogenous Melatonin Improves Fruit Quality Features, Health Promoting Antioxidant Compounds and Yield Traits in Tomato Fruits under Acid Rain Stress

Acid rain is a serious worldwide environmental problem which reduces the growth and yield of crops. Melatonin, as a pleiotropic molecule has been known to improve stress tolerance by limiting the oxidative damage of plants exposed to adverse environments. However, the role of exogenous melatonin particularly on the yield and antioxidant compounds in tomato fruits under abiotic stress condition remains inexpressible. This observation aims to identify the influence of melatonin treatment under simulated acid rain (SAR) condition on fruit qualities, phenolics, flavonoids, and carotenoids concentration in fruits, and yield of tomatoes. Our study results showed that the fruits of SAR-stressed plants had higher quality traits and antioxidant bioactive compounds by increasing antioxidant activities against SAR-induced oxidative stress compared with fruits of control plants. Nonetheless, these improvements to antioxidant activities in fruits under SAR-condition remained unable to prevent the reduction of the yield. However, SAR-stressed plants treated by melatonin exhibited upgradation on the fruit quality traits, antioxidant compounds and yield attributes through accelerating oxidant-scavenging antioxidant actions in fruits compared with fruits of SAR-stressed plants. Meanwhile, our results suggest that exogenous melatonin plays an important role in improvement of bioactive compounds and yield traits in tomato fruits through regulating antioxidant system.

Expression profiling across wild and cultivated tomatoes supports the relevance of early miR482/2118 suppression for Phytophthora resistance

Plants possess a battery of specific pathogen resistance (R-)genes. Precise R-gene regulation is important in the presence and absence of a pathogen. Recently, a microRNA family, miR482/2118, was shown to regulate the expression of a major class of R-genes, nucleotide-binding site leucine-rich repeats (NBS-LRRs). Furthermore, RNA silencing suppressor proteins, secreted by pathogens, prevent the accumulation of miR482/2118, leading to an upregulation of R-genes. Despite this transcriptional release of R-genes, RNA silencing suppressors positively contribute to the virulence of some pathogens. To investigate this paradox, we analysed how the regulation of NBS-LRRs by miR482/2118 has been shaped by the coevolution between Phytophthora infestans and cultivated and wild tomatoes. We used degradome analyses and qRT-PCR to evaluate and quantify the co-expression of miR482/2118 and their NBS-LRR targets. Our data show that miR482/2118-mediated targeting contributes to the regulation of NBS-LRRs in Solanum lycopersicum. Based on miR482/2118 expression profiling in two additional tomato species-with different coevolutionary histories with P. infestans-we hypothesize that pathogen-mediated RNA silencing suppression is most effective in the interaction between S. lycopersicum and P. infestans Furthermore, an upregulation of miR482/2118 early in the infection may increase susceptibility to P. infestans.

Incidence and developmental timing of endosperm failure in post-zygotic isolation between wild tomato lineages

BACKGROUND AND AIMS

Defective hybrid seed development in angiosperms might mediate the rapid establishment of intrinsic post-zygotic isolation between closely related species. Extensive crosses within and among three lineages of wild tomatoes (Solanum section Lycopersicon) were performed to address the incidence, developmental timing and histological manifestations of hybrid seed failure. These lineages encompass different, yet fairly recent, divergence times and both allopatric and partially sympatric pairs.

METHODS

Mature seeds were scored visually 2 months after hand pollinations, and viable-looking seeds were assessed for germination success. Using histological sections from early-developing seeds from a sub-set of crosses, the growth of three major seed compartments (endosperm, embryo and seed coat) was measured at critical developmental stages up to 21 d after pollination, with a focus on the timing and histological manifestations of endosperm misdevelopment in abortive hybrid seeds.

KEY RESULTS

For two of three interspecific combinations including the most closely related pair that was also studied histologically, almost all mature seeds appeared 'flat' and proved inviable; histological analyses revealed impaired endosperm proliferation at early globular embryo stages, concomitant with embryo arrest and seed abortion in both cross directions. The third interspecific combination yielded a mixture of flat, inviable and plump, viable seeds; many of the latter germinated and exhibited near-normal juvenile phenotypes or, in some instances, hybrid necrosis and impaired growth.

CONCLUSIONS

The overall results suggest that near-complete hybrid seed failure can evolve fairly rapidly and without apparent divergence in reproductive phenology/biology. While the evidence accrued here is largely circumstantial, early-acting disruptions of normal endosperm development are most probably the common cause of seed failure regardless of the type of endosperm (nuclear or cellular).

Signatures of natural selection in abiotic stress-responsive genes of Solanum chilense

Environmental conditions are strong selective forces, which may influence adaptation and speciation. The wild tomato species Solanum chilense, native to South America, is exposed to a range of abiotic stress factors. To identify signatures of natural selection and local adaptation, we analysed 16 genes involved in the abiotic stress response and compared the results to a set of reference genes in 23 populations across the entire species range. The abiotic stress-responsive genes are characterized by elevated nonsynonymous nucleotide diversity and divergence. We detected signatures of positive selection in several abiotic stress-responsive genes on both the population and species levels. Local adaptation to abiotic stresses is particularly apparent at the boundary of the species distribution in populations from coastal low-altitude and mountainous high-altitude regions.

Population Genomics in Wild Tomatoes-The Interplay of Divergence and Admixture

Hybridization between closely related plant species is widespread, but the outcomes of hybridization are not fully understood. This study investigates phylogenetic relationships and the history of hybridization in the wild tomato clade (Solanum sect. Lycopersicon). We sequenced RNA from individuals of 38 different populations and, by combining this with published data, build a comprehensive genomic data set for the entire clade. The data indicate that many taxa are not monophyletic and many individuals are admixed due to repeated hybridization. The most polymorphic species, Solanum peruvianum, has two genetic and geographical subpopulations, while its sister species, Solanum chilense, has distinct coastal populations and reduced heterozygosity indicating a recent expansion south following speciation from S. peruvianum circa 1.25 Ma. Discontinuous populations west of 72° are currently described as S. chilense, but are genetically intermediate between S. chilense and S. peruvianum. Based upon molecular, morphological, and crossing data, we test the hypothesis that these discontinuous "S. chilense" populations are an example of recombinational speciation. Recombinational speciation is rarely reported, and we discuss the difficulties in identifying it and differentiating between alternative demographic scenarios. This discovery presents a new opportunity to understand the genomic outcomes of hybridization in plants.

Two Loci Contribute Epistastically to Heterospecific Pollen Rejection, a Postmating Isolating Barrier Between Species

Recognition and rejection of heterospecific male gametes occurs in a broad range of taxa, although the complexity of mechanisms underlying these components of postmating cryptic female choice is poorly understood. In plants, the arena for postmating interactions is the female reproductive tract (pistil), within which heterospecific pollen tube growth can be arrested via active molecular recognition and rejection. Unilateral incompatibility (UI) is one such postmating barrier in which pollen arrest occurs in only one direction of an interspecific cross. We investigated the genetic basis of pistil-side UI between Solanum species, with the specific goal of understanding the role and magnitude of epistasis between UI QTL. Using heterospecific introgression lines (ILs) between Solanum pennellii and S. lycopersicum, we assessed the individual and pairwise effects of three chromosomal regions (ui1.1, ui3.1, and ui12.1) previously associated with interspecific UI among Solanum species. Specifically, we generated double introgression (‘pyramided’) genotypes that combined ui12.1 with each of ui1.1 and ui3.1, and assessed the strength of UI pollen rejection in the pyramided lines, compared to single introgression genotypes. We found that none of the three QTL individually showed UI rejection phenotypes, but lines combining ui3.1 and ui12.1 showed significant pistil-side pollen rejection. Furthermore, double ILs (DILs) that combined different chromosomal regions overlapping ui3.1 differed significantly in their rate of UI, consistent with at least two genetic factors on chromosome three contributing quantitatively to interspecific pollen rejection. Together, our data indicate that loci on both chromosomes 3 and 12 are jointly required for the expression of UI between S. pennellii and S. lycopersicum, suggesting that coordinated molecular interactions among a relatively few loci underlie the expression of this postmating prezygotic barrier. In addition, in conjunction with previous data, at least one of these loci appears to also contribute to conspecific self-incompatibility (SI), consistent with a partially shared genetic basis between inter- and intraspecific mechanisms of postmating prezygotic female choice.

Weak coordination between leaf structure and function among closely related tomato species

Theory predicts that natural selection should favor coordination between leaf physiology, biochemistry and anatomical structure along a functional trait spectrum from fast, resource-acquisitive syndromes to slow, resource-conservative syndromes. However, the coordination hypothesis has rarely been tested at a phylogenetic scale most relevant for understanding rapid adaptation in the recent past or for the prediction of evolutionary trajectories in response to climate change. We used a common garden to examine genetically based coordination between leaf traits across 19 wild and cultivated tomato taxa. We found weak integration between leaf structure (e.g. leaf mass per area) and physiological function (photosynthetic rate, biochemical capacity and CO₂ diffusion), even though all were arrayed in the predicted direction along a 'fast-slow' spectrum. This suggests considerable scope for unique trait combinations to evolve in response to new environments or in crop breeding. In particular, we found that partially independent variation in stomatal and mesophyll conductance may allow a plant to improve water-use efficiency without necessarily sacrificing maximum photosynthetic rates. Our study does not imply that functional trait spectra, such as the leaf economics spectrum, are unimportant, but that many important axes of variation within a taxonomic group may be unique and not generalizable to other taxa.

Heat Stress Decreases Levels of Nutrient-Uptake and -Assimilation Proteins in Tomato Roots

Global warming will increase root heat stress, which is already common under certain conditions. Effects of heat stress on root nutrient uptake have rarely been examined in intact plants, but the limited results indicate that heat stress will decrease it; no studies have examined heat-stress effects on the concentration of nutrient-uptake proteins. We grew Solanum lycopersicum (tomato) at 25 °C/20 °C (day/night) and then transferred some plants for six days to 35 °C /30 °C (moderate heat) or 42 °C/37 °C (severe heat) (maximum root temperature = 32 °C or 39 °C, respectively); plants were then moved back to control conditions for seven days to monitor recovery. In a second experiment, plants were grown for 15 days at 28 °C/23 °C, 32 °C/27 °C, 36 °C/31 °C, and 40 °C/35 °C (day/night). Concentrations of nutrient-uptake and -assimilation proteins in roots were determined using protein-specific antibodies and ELISA (enzyme-linked immunosorbent assay). In general, (1) roots were affected by heat more than shoots, as indicated by decreased root:shoot mass ratio, shoot vs. root %N and C, and the level of nutrient metabolism proteins vs. less sensitive photosynthesis and stomatal conductance; and (2) negative effects on roots were large and slow-to-recover only with severe heat stress (40 °C-42 °C). Thus, short-term heat stress, if severe, can decrease total protein concentration and levels of nutrient-uptake and -assimilation proteins in roots. Hence, increases in heat stress with global warming may decrease crop production, as well as nutritional quality, partly via effects on root nutrient relations.

Tomato Reproductive Success Is Equally Affected by Herbivores That Induce or That Suppress Defenses

Herbivory induces plant defenses. These responses are often costly, yet enable plants under attack to reach a higher fitness than they would have reached without these defenses. Spider mites (Tetranychus ssp.) are polyphagous plant-pests. While most strains of the species Tetranychus urticae induce defenses at the expense of their performance, the species Tetranychus evansi suppresses plant defenses and thereby maintains a high performance. Most data indicate that suppression is a mite-adaptive trait. Suppression is characterized by a massive down-regulation of plant gene-expression compared to plants infested with defense-inducing mites as well as compared to control plants, albeit to a lesser extent. Therefore, we hypothesized that suppression may also benefit a plant since the resources saved during down-regulation could be used to increase reproduction. To test this hypothesis, we compared fruit and viable seed production of uninfested tomato plants with that of plants infested with defense-inducing or defense-suppressing mites. Mite-infested plants produced fruits faster than control plants albeit in lower total amounts. The T. evansi-infested plants produced the lowest number of fruits. However, the number of viable seeds was equal across treatments at the end of the experiment. Nonetheless, at this stage control plants were still alive and productive and therefore reach a higher lifetime fitness than mite-infested plants. Our results indicate that plants have plastic control over reproduction and can speed up fruit- and seed production when conditions are unfavorable. Moreover, we showed that although suppressed plants are less productive in terms of fruit production than induced plants, their lifetime fitness was equal under laboratory conditions. However, under natural conditions the fitness of plants such as tomato will also depend on the efficiency of seed dispersal by animals. Hence, we argue that the fitness of induced plants in the field may be promoted more by their higher fruit production relative to that of their suppressed counterparts.

Mating system transitions in Solanum habrochaites impact interactions between populations and species

In plants, transitions in mating system from outcrossing to self-fertilization are common; however, the impact of these transitions on interspecific and interpopulation reproductive barriers is not fully understood. We examined the consequences of mating system transition for reproductive barriers in 19 populations of the wild tomato species Solanum habrochaites. We identified S. habrochaites populations with self-incompatible (SI), self-compatible (SC) and mixed population (MP) mating systems, and characterized pollen-pistil interactions among S. habrochaites populations and between S. habrochaites and other tomato species. We examined the relationship between mating system, floral morphology, interspecific and interpopulation compatibility and pistil SI factors. We documented five distinct phenotypic groups by combining reproductive behavior with molecular data. Transitions from SI to MP were not associated with weakened interspecific reproductive barriers or loss of known pistil SI factors. However, transitions to SC at the northern range margin were accompanied by loss of S-RNase, smaller flowers, and weakened (or absent) interspecific pollen-pistil barriers. Finally, we identified a subset of SC populations that exhibited a partial interpopulation reproductive barrier with central SI populations. Our results support the hypothesis that shifts in mating system, followed by additional loss-of-function mutations, impact reproductive barriers within and between species.

Interspecific reproductive barriers between sympatric populations of wild tomato species (Solanum section Lycopersicon)

PREMISE OF THE STUDY

Interspecific reproductive barriers (IRBs) often prevent hybridization between closely related species in sympatry. In the tomato clade (Solanum section Lycopersicon), interspecific interactions between natural sympatric populations have not been evaluated previously. In this study, we assessed IRBs between members of the tomato clade from nine sympatric sites in Peru.

METHODS

Coflowering was assessed at sympatric sites in Peru. Using previously collected seeds from sympatric sites in Peru, we evaluated premating prezygotic (floral morphology), postmating prezygotic (pollen-tube growth), and postzygotic barriers (fruit and seed development) between sympatric species in common gardens. Pollen-tube growth and seed development were examined in reciprocal crosses between sympatric species.

KEY RESULTS

We confirmed coflowering of sympatric species at five sites in Peru. We found three types of postmating prezygotic IRBs during pollen-pistil interactions: (1) unilateral pollen-tube rejection between pistils of self-incompatible species and pollen of self-compatible species; (2) potential conspecific pollen precedence in a cross between two self-incompatible species; and (3) failure of pollen tubes to target ovules. In addition, we found strong postzygotic IRBs that prevented normal seed development in 11 interspecific crosses, resulting in seed-like structures containing globular embryos and aborted endosperm and, in some cases, overgrown endothelium. Viable seed and F₁ hybrid plants were recovered from three of 19 interspecific crosses.

CONCLUSIONS

We have identified diverse prezygotic and postzygotic IRBs that would prevent hybridization between sympatric wild tomato species, but interspecific hybridization is possible in a few cases.

A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

Adaptation to low temperatures in the wild tomato species Solanum chilense

Molecular adaptation to abiotic stresses in plants is a complex process based mainly on the modifications of gene transcriptional activity and the alteration of protein-protein interactions. We used a combination of population genetic, comparative transcriptomic and plant physiology approaches to investigate the mechanisms of adaptation to low temperatures in Solanum chilense populations distributed along Andean altitudinal gradients. We found that plants from all populations have high chilling tolerance, which does not correlate with temperatures in their native habitats. In contrast, tolerance to freezing shows a significant association with altitude and temperature variables. We also observed the differences in expression patterns of cold-response genes between plants from high- and low-altitude populations. These results suggest that genetic adaptations to low temperatures evolved in high-altitude populations of S. chilense. At the transcriptional level, these adaptations may include high levels of constitutive expression of the genes encoding ICE1, the key transcription factor of the cold signalling pathway, and chloroplast ω-3 fatty acid desaturase FAD7. At the sequence level, a signature of selection associated with the adaptation to high altitudes was detected at the C-terminal part of ICE1 encoding the ACT regulatory domain.

The yellow-fruited tomato 1 (yft1) mutant has altered fruit carotenoid accumulation and reduced ethylene production as a result of a genetic lesion in ETHYLENE INSENSITIVE2

The isolated yft1 allele controls the formation of fruit color in n3122 via the regulation of response to ethylene, carotenoid accumulation and chromoplast development. Fruit color is one of the most important quality traits of tomato (Solanum lycopersicum) and is closely associated with both nutritional and market value. In this study, we characterized a tomato fruit color mutant n3122, named as yellow-fruited tomato 1 (yft1), which produces yellow colored mature fruit. Fruit color segregation of the progeny from an intra-specific cross (M82 × n3122) and an inter-specific cross (n3122 × LA1585) revealed that a single recessive nuclear gene determined the yellow fruit phenotype. Through map-based cloning, the yft1 locus was assigned to an 88.2 kb region at the top of chromosome 9 that was annotated as containing 12 genes. Sequencing revealed that one gene, Solyc09g007870, which encodes ETHYLENE INSENSITIVE2 (EIN2), contained two mutations in yft1: a 13 bp deletion and a 573 bp insertion at position -318 bp upstream of the translation initiation site. We detected that EIN2 expression was substantially lower in yft1 than in the red-fruited M82 wild type and that, in addition, carotenoid accumulation was decreased, ethylene synthesis and perception were impaired and chromoplast development was delayed. The results implied that the reduced expression of EIN2 in yft1 leads to suppressed ethylene signaling which results in abnormal carotenoid production.

A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants

The Enhancer of Zeste Polycomb group proteins, which are encoded by a small gene family in Arabidopsis thaliana, participate to the control of plant development. In the tomato (Solanum lycopersicum), these proteins are encoded by three genes (SlEZ1, SlEZ2 and SlEZ3) that display specific expression profiles. Using a gene specific RNAi strategy, we demonstrate that repression of SlEZ2 correlates with a general reduction of H3K27me3 levels, indicating that SlEZ2 is part of an active PRC2 complex. Reduction of SlEZ2 gene expression impacts the vegetative development of tomato plants, consistent with SlEZ2 having retained at least some of the functions of the Arabidopsis CURLY LEAF (CLF) protein. Notwithstanding, we observed significant differences between transgenic SlEZ2 RNAi tomato plants and Arabidopsis clf mutants. First, we found that reduced SlEZ2 expression has dramatic effects on tomato fruit development and ripening, functions not described in Arabidopsis for the CLF protein. In addition, repression of SlEZ2 has no significant effect on the flowering time or the control of flower organ identity, in contrast to the Arabidopsis clf mutation. Taken together, our results are consistent with a diversification of the function of CLF orthologues in plants, and indicate that although partly conserved amongst plants, the function of EZ proteins need to be newly investigated for non-model plants because they might have been recruited to specific developmental processes.

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

Constraint around Quarter-Power Allometric Scaling in Wild Tomatoes (Solanum sect. Lycopersicon; Solanaceae)

The West-Brown-Enquist (WBE) metabolic scaling theory posits that many organismal features scale predictably with body size because of selection to minimize transport costs in resource distribution networks. Many scaling exponents are quarter-powers, as predicted by WBE, but there are also biologically significant deviations that could reflect adaptation to different environments. A central but untested prediction of the WBE model is that wide deviation from optimal scaling is penalized, leading to a pattern of constraint on scaling exponents. Here, we demonstrate, using phylogenetic comparative methods, that variation in allometric scaling between mass and leaf area across 17 wild tomato taxa is constrained around a value indistinguishable from that predicted by WBE but significantly greater than 2/3 (geometric-similarity model). The allometric-scaling exponent was highly correlated with fecundity, water use, and drought response, suggesting that it is functionally significant and therefore could be under selective constraints. However, scaling was not strictly log-log linear but rather declined during ontogeny in all species, as has been observed in many plant species. We caution that although our results supported one prediction of the WBE model, it did not strongly test the model in other important respects. Nevertheless, phylogenetic comparative methods such as those used here are powerful but underutilized tools for metabolic ecology that complement existing methods to adjudicate between models.

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.

Morphological and anatomical determinants of mesophyll conductance in wild relatives of tomato (Solanum sect. Lycopersicon, sect. Lycopersicoides; Solanaceae)

Natural selection on photosynthetic performance is a primary factor determining leaf phenotypes. The complex CO2 diffusion path from substomatal cavities to the chloroplasts - the mesophyll conductance (g(m)) - limits photosynthetic rate in many species and hence shapes variation in leaf morphology and anatomy. Among sclerophyllous and succulent taxa, structural investment in leaves, measured as the leaf dry mass per area (LMA), has been implicated in decreased gm . However, in herbaceous taxa with high g(m), it is less certain how LMA impacts CO2 diffusion and whether it significantly affects photosynthetic performance. We addressed these questions in the context of understanding the ecophysiological significance of leaf trait variation in wild tomatoes, a closely related group of herbaceous perennials. Although g(m) was high in wild tomatoes, variation in g(m) significantly affected photosynthesis. Even in these tender-leaved herbaceous species, greater LMA led to reduced g(m). This relationship between g(m) and LMA is partially mediated by cell packing and leaf thickness, although amphistomy (equal distribution of stomata on both sides of the leaf) mitigates the effect of leaf thickness. Understanding the costs of increased LMA will inform future work on the adaptive significance of leaf trait variation across ecological gradients in wild tomatoes and other systems.

From genome to phenome and back in tomato

The tomato is an ideal plant species for genomic and evolutionary studies. Thanks to recent technical advances, a plethora of information relating to tomato genomics has been generated. In addition, various phenotypes related to morphology, physiology and yield have been investigated in tomato and its wild relatives. In this review, we summarize recent key findings in tomato genomics that used both developmental and evolutionary approaches to link the genome to phenome. Combined, these perspectives allow us to look at the trends in tomato evolution in addition to providing insight into the future direction of research that can utilize this unique model species.

Comparative genome analysis of Solanum lycopersicum and Solanum tuberosum

Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato.

Sequence evolution and expression regulation of stress-responsive genes in natural populations of wild tomato

The wild tomato species Solanum chilense and S. peruvianum are a valuable non-model system for studying plant adaptation since they grow in diverse environments facing many abiotic constraints. Here we investigate the sequence evolution of regulatory regions of drought and cold responsive genes and their expression regulation. The coding regions of these genes were previously shown to exhibit signatures of positive selection. Expression profiles and sequence evolution of regulatory regions of members of the Asr (ABA/water stress/ripening induced) gene family and the dehydrin gene pLC30-15 were analyzed in wild tomato populations from contrasting environments. For S. chilense, we found that Asr4 and pLC30-15 appear to respond much faster to drought conditions in accessions from very dry environments than accessions from more mesic locations. Sequence analysis suggests that the promoter of Asr2 and the downstream region of pLC30-15 are under positive selection in some local populations of S. chilense. By investigating gene expression differences at the population level we provide further support of our previous conclusions that Asr2, Asr4, and pLC30-15 are promising candidates for functional studies of adaptation. Our analysis also demonstrates the power of the candidate gene approach in evolutionary biology research and highlights the importance of wild Solanum species as a genetic resource for their cultivated relatives.