Differences in insect resistance between tomato species endemic to the Galapagos Islands

De novo domestication in the Solanaceae: advances and challenges

The advent of highly efficient genome editing (GE) tools, coupled with high-throughput genome sequencing, has paved the way for the accelerated domestication of crop wild relatives. New crops could thus be rapidly created that are well adapted to cope with drought, flooding, soil salinity, or insect damage. De novo domestication avoids the complexity of transferring polygenic stress resistance from wild species to crops. Instead, new crops can be created by manipulating major genes in stress-resistant wild species. However, the genetic basis of certain relevant domestication-related traits often involve epistasis and pleiotropy. Furthermore, pan-genome analyses show that structural variation driving gene expression changes has been selected during domestication. A growing body of work suggests that the Solanaceae family, which includes crop species such as tomatoes, potatoes, eggplants, peppers, and tobacco, is a suitable model group to dissect these phenomena and operate changes in wild relatives to improve agronomic traits rapidly with GE. We briefly discuss the prospects of this exciting novel field in the interface between fundamental and applied plant biology and its potential impact in the coming years.

The amount and chemistry of acylsugars affects sweetpotato whitefly (Bemisia tabaci) oviposition and development, and tomato yellow leaf curl virus incidence, in field grown tomato plants

The objectives of this study were to ascertain the impact of endogenous production of trichome-exuded acylsugars on insects and insect transmitted virus by evaluating tomato lines and their hybrids bred for acylsugar production under field settings on whiteflies and the whitefly-transmitted tomato yellow leaf curl virus. Specifically, we utilized a diverse array of tomato lines and hybrids bred for changes in acylsugar amount or type, grown in three field trials under natural whitefly and virus pressure, to investigate whether the amount of accumulated acylsugars and or the chemical profile of the acylsugars were associated with greater resistance to whiteflies and reduced incidence of tomato yellow leaf curl virus. There was considerable variation in the abundance of whitefly eggs and nymphs and incidence of tomato yellow leaf curl virus across experiments and between entries. Increasing amount of acylsugars accumulated by the tomato entries was associated with a reduction in the abundance of whitefly eggs and nymphs and a reduction in the incidence of tomato yellow leaf curl virus. Additionally, we identified lines with changes in several acylsugar fatty acids that were associated with decreased abundance of whitefly eggs and nymphs and reduced incidence of tomato yellow leaf curl virus. These results inform the utility of acylsugars as a host plant defense system for improving resistance to whiteflies and their transmitted viruses, with potential for reducing insecticides as a control method for whiteflies and provide breeding targets for optimization of existing acylsugar tomato lines to create lines with the most efficacious amount and chemistry of acylsugars.

Induction of Glandular Trichomes to Control Bemisia tabaci in Tomato Crops: Modulation by the Natural Enemy Nesidiocoris tenuis

Whitefly-transmitted viruses are one of the biggest threats to tomato (Solanum lycopersicum) growing worldwide. Strategies based on the introgression of resistance traits from wild relatives are promoted to control tomato pests and diseases. Recently, a trichome-based resistance characterizing the wild species Solanum pimpinellifolium was introgressed into a cultivated tomato. An advanced backcross line (BC5S2) exhibiting the presence of acylsugar-associated type IV trichomes, which are lacking in cultivated tomatoes, was effective at controlling whiteflies (Hemiptera: Aleyrodidae) and limiting the spread of whitefly-transmitted viruses. However, at early growth stages, type IV trichome density and acylsugar production are limited; thus, protection against whiteflies and whitefly-transmitted viruses remains irrelevant. In this work, we demonstrate that young BC5S2 tomato plants feeding-punctured by the zoophytophagous predator Nesidiocoris tenuis (Hemiptera: Miridae) displayed an increase (above 50%) in type IV trichome density. Acylsugar production was consistently increased in N. tenuis-punctured BC5S2 plants, which was more likely associated with upregulated expression of the BCKD-E2 gene related to acylsugar biosynthesis. In addition, the infestation of BC5S2 plants with N. tenuis effectively induced the expression of defensive genes involved in the jasmonic acid signaling pathway, resulting in strong repellence to Bemisia tabaci and attractiveness to N. tenuis. Thus, through preplant release of N. tenuis in tomato nurseries carried out in some integrated pest management programs, type IV trichome-expressing plants can be prepared to control whiteflies and whitefly-transmitted viruses at early growth stages. This study emphasizes the advantage of reinforcing constitutive resistance using defense inducers to guarantee robust protection against pests and transmitted viruses.

Acylsugar-mediated resistance as part of a multilayered defense against thrips, orthotospoviruses, and beyond

Resistant varieties are critical tools for crop production, and single-resistance genes providing strong protection against pests or pathogens are deployed in agriculture. Durability of these traits is threatened by emergence of resistance-breaking pests and pathogens. This review focuses on acylsugar-mediated resistance in tomato. Wild tomatoes have type-IV trichomes that exude chemically complex mixtures of acylsugars altering behavior and suppressing multiple pest species, and with thrips and whiteflies (WF), suppressing virus transmission, for example, Tomato spotted wilt orthotospovirus and Tomato yellow leaf curl virus, respectively. Marker-assisted selection and bioassays led to development of advanced cultivated tomato breeding lines rich in acylsugar variations, allowing acylsugar-mediated resistance to be combined with other resistance traits providing a layered defense system that reduces pest populations and virus disease prevalence. This strategy also holds promise for enhancing durability of virus resistance genes by reducing the intensity of selection for resistance-breaking variants.

Evaluation of Ecuadorian genotypes of Capsicum spp. against infestations of Bemisia tabaci

The genus Capsicum, native to tropical and subtropical America, belongs to the Solanaceae family, which includes commercially important vegetables such as chilies and green peppers. The silverleaf whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), causes losses to vegetables including Capsicum species. Among the alternatives of pest control, an effective, economical, and environmentally compatible method is the resistance of the host plant. Infestation by B. tabaci was evaluated in 73 Capsicum genotypes, corresponding to the species C. annuum, C. baccatum, C. sinense, C. frutescens and C. pubescens from an Ecuadorian genebank. Eighty-four percent of the C. baccatum genotypes evaluated showed the highest population densities of B. tabaci, while all the genotypes of C. sinense and C. frutescens had the lowest values (p < 0.05). The non-preference of adults and the scarce oviposition of B. tabaci on genotypes of C. sinense and C. frutescens suggests resistance due to antixenosis. These results could guide breeding programs for the resistance of Capsicum species to B. tabaci infestations.

Multifunctional Contribution of the Inflated Fruiting Calyx: Implication for Cuticular Barrier Profiles of the Solanaceous Genera Physalis, Alkekengi, and Nicandra

Pivotal barrier properties of the hydrophobic plant cuticle covering aerial plant surfaces depend on its physicochemical composition. Among plant species and organs, compounds of this boundary layer between the plant interior and the environment vary considerably but cuticle-related studies comparing different organs from the same plant species are still scarce. Thus, this study focused on the cuticle profiles of Physalis peruviana, Physalis ixocarpa, Alkekengi officinarum, and Nicandra physalodes species. Inflated fruiting calyces enveloping fruits make Physalis, Alkekengi, and Nicandra highly recognizable genera among the Solanoideae subfamily. Although the inflation of fruiting calyces is well discussed in the literature still little is known about their post-floral functionalities. Cuticular composition, surface structure, and barrier function were examined and compared in fully expanded amphistomatous leaves, ripe astomatous fruits, and fully inflated hypostomatous fruiting calyces. Species- and organ-specific abundances of non-glandular and glandular trichomes revealed high structural diversity, covering not only abaxial and adaxial leaf surfaces but also fruiting calyx surfaces, whereas fruits were glabrous. Cuticular waxes, which limit non-stomatal transpiration, ranged from <1 μg cm^-2 on P. peruviana fruiting calyces and N. physalodes fruits to 22 μg cm^-2 on P. peruviana fruits. Very-long-chain aliphatic compounds, notably n-alkanes, iso-, and anteiso-branched alkanes, alkanols, alkanoic acids, and alkyl esters, dominated the cuticular wax coverages (≥86%). Diversity of cuticular wax patterns rose from leaves to fruiting calyces and peaked in fruits. The polymeric cutin matrix providing the structural framework for cuticular waxes was determined to range from 81 μg cm^-2 for N. physalodes to 571 μg cm^-2 for A. officinarum fruits. Cuticular transpiration barriers were highly efficient, with water permeabilities being ≤5 × 10^-5 m s^-1. Only the cuticular water permeability of N. physalodes fruits was 10 × 10^-5 m s^-1 leading to their early desiccation and fruits that easily split, whereas P. peruviana, P. ixocarpa, and A. officinarum bore fleshy fruits for extended periods after maturation. Regarding the functional significance, fruiting calyces establish a physicochemical shield that reduces water loss and enables fruit maturation within a protective microclimate, and promotes different seed dispersal strategies among plant species investigated.

Functional characterization of the tomato HAIRPLUS gene reveals the implication of the epigenome in the control of glandular trichome formation

Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and confer trichomes a key role in the defence against herbivores. In this work, the tomato gene HAIRPLUS (HAP) that controls glandular trichome density in tomato plants was characterised. HAP belongs to a group of proteins involved in histone tail modifications although some also bind methylated DNA. HAP loss of function promotes epigenomic modifications in the tomato genome reflected in numerous differentially methylated cytosines and causes transcriptomic changes in hap mutant plants. Taken together, these findings demonstrate that HAP links epigenome remodelling with multicellular glandular trichome development and reveal that HAP is a valuable genomic tool for pest resistance in tomato breeding.

Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach

BACKGROUND

Plant-produced specialised metabolites are a powerful part of a plant's first line of defence against herbivorous insects, bacteria and fungi. Wild ancestors of present-day cultivated tomato produce a plethora of acylsugars in their type-I/IV trichomes and volatiles in their type-VI trichomes that have a potential role in plant resistance against insects. However, metabolic profiles are often complex mixtures making identification of the functionally interesting metabolites challenging. Here, we aimed to identify specialised metabolites from a wide range of wild tomato genotypes that could explain resistance to vector insects whitefly (Bemisia tabaci) and Western flower thrips (Frankliniella occidentalis). We evaluated plant resistance, determined trichome density and obtained metabolite profiles of the glandular trichomes by LC-MS (acylsugars) and GC-MS (volatiles). Using a customised Random Forest learning algorithm, we determined the contribution of specific specialised metabolites to the resistance phenotypes observed.

RESULTS

The selected wild tomato accessions showed different levels of resistance to both whiteflies and thrips. Accessions resistant to one insect can be susceptible to another. Glandular trichome density is not necessarily a good predictor for plant resistance although the density of type-I/IV trichomes, related to the production of acylsugars, appears to correlate with whitefly resistance. For type VI-trichomes, however, it seems resistance is determined by the specific content of the glands. There is a strong qualitative and quantitative variation in the metabolite profiles between different accessions, even when they are from the same species. Out of 76 acylsugars found, the random forest algorithm linked two acylsugars (S3:15 and S3:21) to whitefly resistance, but none to thrips resistance. Out of 86 volatiles detected, the sesquiterpene α-humulene was linked to whitefly susceptible accessions instead. The algorithm did not link any specific metabolite to resistance against thrips, but monoterpenes α-phellandrene, α-terpinene and β-phellandrene/D-limonene were significantly associated with susceptible tomato accessions.

CONCLUSIONS

Whiteflies and thrips are distinctly targeted by certain specialised metabolites found in wild tomatoes. The machine learning approach presented helped to identify features with efficacy toward the insect species studied. These acylsugar metabolites can be targets for breeding efforts towards the selection of insect-resistant cultivars.

Resistance Sources and Antixenotic Factors in Brazilian Bean Genotypes Against Bemisia tabaci

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Middle East Asia Minor 1 is one of the most important pests of the common bean, due to its potential of causing direct and indirect damage. This study aimed to evaluate 78 bean genotypes to verify the occurrence of resistance of antixenosis type against B. tabaci. Initially, multiple-choice trials were performed to evaluate the oviposition preference and nymphs' establishment at 3 and 15 days after infestation. Subsequently, 21 bean genotypes were selected, and a no-choice test was conducted. Colorimetric analyses were performed to establish correlations between leaf color and insect establishment. In multiple-choice trial, the genotypes BRS Ametista, BRS Estilo, BRS Esplendor, SCS 204 Predileto, BRS Notável, IPR Eldorado, CHIB 06, IPR Quero-Quero, Iapar 81, CHIP 338, IPR Garça, Arcelina 4, SCS 202 Guará, IAC Esperança, H96102-1-1-1-52, CHIP 348, Carioca Comum, CHIP 300, IAC Carioca Eté, IAC Ybaté, and Tybatã were the least used for oviposition and nymph establishment, demonstrating antixenosis or antibiosis. In the no-choice trial, most genotypes were less attractive to whitefly, and the genotypes CHIB 06, IPR Garça, CHIP 300, and IAC Esperança had less oviposition. The most attractive genotypes presented high luminosity and more intense green and yellow colors, indicating positive correlation. Therefore, the genotypes BRS Ametista, SCS 204 Predileto, BRS Estilo, IPR Eldorado, SCS-202 Guará, Carioca Comum, Arcelina 4, CHIP 348, and IAC Esperança showed the highest resistance stability in the no-choice trial, and they are promising sources of antixenotic factors for use in breeding programs to obtain whitefly-resistant common bean lines.

Glandular trichomes: micro-organs with model status?

Glandular trichomes are epidermal outgrowths that are the site of biosynthesis and storage of large quantities of specialized metabolites. Besides their role in the protection of plants against biotic and abiotic stresses, they have attracted interest owing to the importance of the compounds they produce for human use; for example, as pharmaceuticals, flavor and fragrance ingredients, or pesticides. Here, we review what novel concepts investigations on glandular trichomes have brought to the field of specialized metabolism, particularly with respect to chemical and enzymatic diversity. Furthermore, the next challenges in the field are understanding the metabolic network underlying the high productivity of glandular trichomes and the transport and storage of metabolites. Another emerging area is the development of glandular trichomes. Studies in some model species, essentially tomato, tobacco, and Artemisia, are now providing the first molecular clues, but many open questions remain: How is the distribution and density of different trichome types on the leaf surface controlled? When is the decision for an epidermal cell to differentiate into one type of trichome or another taken? Recent advances in gene editing make it now possible to address these questions and promise exciting discoveries in the near future.

Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives

This study provides insights in patterns of distribution of abiotic and biotic stress resilience across Vigna gene pools to enhance the use and conservation of these genetic resources for legume breeding. Vigna is a pantropical genus with more than 88 taxa including important crops such as V. radiata (mung bean) and V. unguiculata (cowpea). Our results show that sources of pest and disease resistance occur in at least 75 percent of the Vigna taxa, which were part of screening assessments, while sources of abiotic stress resilience occur in less than 30 percent of screened taxa. This difference in levels of resilience suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses because of short growing seasons or with taxa, which tolerate salinity. We recommend prioritizing these rare Vigna taxa for conservation and screening for combined abiotic and biotic stress resilience resulting from stacked or multifunctional traits. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that will suffer from salinization under global climate change.

Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives

This study provides insights in patterns of distribution of abiotic and biotic stress resilience across Vigna gene pools to enhance the use and conservation of these genetic resources for legume breeding. Vigna is a pantropical genus with more than 88 taxa including important crops such as V. radiata (mung bean) and V. unguiculata (cowpea). Our results show that sources of pest and disease resistance occur in at least 75 percent of the Vigna taxa, which were part of screening assessments, while sources of abiotic stress resilience occur in less than 30 percent of screened taxa. This difference in levels of resilience suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses because of short growing seasons or with taxa, which tolerate salinity. We recommend prioritizing these rare Vigna taxa for conservation and screening for combined abiotic and biotic stress resilience resulting from stacked or multifunctional traits. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that will suffer from salinization under global climate change.

QTL mapping of insect resistance components of Solanum galapagense

QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In tomato, resistance towards insects is found in wild relatives and has been attributed to the presence of glandular trichomes and their specific phytochemical composition. In this paper, we describe the results from a large-scale QTL mapping of data from whitefly resistance tests, trichome phenotyping and a comprehensive metabolomics analysis in a recombinant inbred line population derived from a cross between the cultivated Solanum lycopersicum and the wild relative S. galapagense, which is resistant to a range of pest insects. One major QTL (Wf-1) was found to govern the resistance against two different whitefly species. This QTL co-localizes with QTLs for the presence of trichomes type IV and V, as well as all 76 acyl sugars detected and about 150 other non-volatile phytochemicals, including methyl esters of the flavonols myricetin and quercetin. Based on these results, we hypothesize that Wf-1 is regulating the formation of glandular trichome type IV on the leaf epidermis, enabling the production and accumulation of bioactive metabolites in this type of trichomes.

Broad spectrum insect resistance and metabolites in close relatives of the cultivated tomato

Wild relatives of tomato possess effective means to deal with several pests, among which are a variety of insects. Here we studied the presence of resistance components against Trialeurodes vaporariorum, Myzus persicae, Frankliniella occidentalis, and Spodoptera exigua in the Lycopersicon group of Solanum section Lycopersicon by means of bioassays and comprehensive metabolite profiling. Broad spectrum resistance was found in Solanum galapagense and a few accessions of S. pimpinellifolium. Resistance to the sap sucking insects may be based on the same mechanism, but different from the caterpillar resistance. Large and highly significant differences in the leaf metabolomes were found between S. galapagense, containing type IV trichomes, and its closest relative S. cheesmaniae, which lacks type IV trichomes. The most evident differences were the relatively high levels of different methylated forms of the flavonoid myricetin and many acyl sucrose structures in S. galapagense. Possible candidate genes regulating the production of these compounds were identified in the Wf-1 QTL region of S. galapagense, which was previously shown to confer resistance to the whitefly B. tabaci. The broad spectrum insect resistance identified in S. galapagense will be very useful to increase resistance in cultivated tomato.

Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping

Background

Cultivated tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potato and a member of thirteen interfertile species of Solanum genus. Domestication and continuous selection for desirable traits made cultivated tomato species susceptible to many stresses as compared to the wild species. In this study, we analyzed and compared the genomes of wild and cultivated tomato accessions to identify the genomic regions that encountered changes during domestication.

Results

Analysis was based on SNP and InDel mining of twentynine accessions of twelve wild tomato species and forty accessions of cultivated tomato. Percentage of common SNPs among the accessions within a species corresponded with the reproductive behavior of the species. SNP profiles of the wild tomato species within a phylogenetic subsection varied with their geographical distribution. Interestingly, the ratio of genic SNP to total SNPs increased with phylogenetic distance of the wild tomato species from the domesticated species, suggesting that variations in gene-coding region play a major role in speciation. We retrieved 2439 physical positions in 1594 genes including 32 resistance related genes where all the wild accessions possessed a common wild variant allele different from all the cultivated accessions studied. Tajima’s D analysis predicted a very strong purifying selection associated with domestication in nearly 1% of its genome, half of which is contributed by chromosome 11. This genomic region with a low Tajima’s D value hosts a variety of genes associated with important agronomic trait such as, fruit size, tiller number and wax deposition.

Conclusion

Our analysis revealed a broad-spectrum genetic base in wild tomato species and erosion of that in cultivated tomato due to recurrent selection for agronomically important traits. Identification of the common wild variant alleles and the genomic regions undergoing purifying selection during cultivation would facilitate future breeding program by introgression from wild species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3822-3) contains supplementary material, which is available to authorized users.

Loss of type-IV glandular trichomes is a heterochronic trait in tomato and can be reverted by promoting juvenility

Glandular trichomes are structures with widespread distribution and deep ecological significance. In the Solanum genus, type-IV glandular trichomes provide resistance to insect pests. The occurrence of these structures is, however, poorly described and controversial in cultivated tomato (Solanum lycopersicum). Optical and scanning electron microscopy were used to screen a series of well-known commercial tomato cultivars, revealing the presence of type-IV trichomes on embryonic (cotyledons) and juvenile leaves. A tomato line overexpressing the microRNA miR156, known to promote heterochronic development, and mutants affecting KNOX and CLAVATA3 genes possessed type-IV trichomes in adult leaves. A re-analysis of the Woolly (Wo) mutant, previously described as enhancing glandular trichome density, showed that this effect only occurs at the juvenile phase of vegetative development. Our results suggest the existence of at least two levels of regulation of multicellular trichome formation in tomato: one enhancing different types of trichomes, such as that controlled by the WOOLLY gene, and another dependent on developmental stage, which is fundamental for type-IV trichome formation. Their combined manipulation could represent an avenue for biotechnological engineering of trichome development in plants.

Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape

Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.

Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: Case study in tomato

The ideotype is a theoretical model of an archetypal cultivated plant. Recent progress in genome editing is aiding the pursuit of this ideal in crop breeding. Breeding is relatively straightforward when the traits in question are monogenic in nature and show Mendelian inheritance. Conversely, traits with a diffuse, polygenic basis such as abiotic stress resistance are more difficult to harness. In recent years, many genes have been identified that are important for plant domestication and act by increasing yield, grain or fruit size or altering plant architecture. Here, we propose that (a) key monogenic traits whose physiology has been unveiled can be molecularly tailored to achieve the ideotype; and (b) wild relatives of crops harboring polygenic stress resistance genes or other traits of interest could be de novo domesticated by manipulating monogenic yield-related traits through state-of-the-art gene editing techniques. An overview of the genomic and physiological challenges in the world's main staple crops is provided. We focus on tomato and its wild Solanum (section Lycopersicon) relatives as a suitable model for molecular design in the pursuit of the ideotype for elite cultivars and to test de novo domestication of wild relatives.

Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

Quantitative resistance against Bemisia tabaci in Solanum pennellii: Genetics and metabolomics

The whitefly Bemisia tabaci is a serious threat in tomato cultivation worldwide as all varieties grown today are highly susceptible to this devastating herbivorous insect. Many accessions of the tomato wild relative Solanum pennellii show a high resistance towards B. tabaci. A mapping approach was used to elucidate the genetic background of whitefly-resistance related traits and associated biochemical traits in this species. Minor quantitative trait loci (QTLs) for whitefly adult survival (AS) and oviposition rate (OR) were identified and some were confirmed in an F2 BC1 population, where they showed increased percentages of explained variance (more than 30%). Bulked segregant analyses on pools of whitefly-resistant and -susceptible F2 plants enabled the identification of metabolites that correlate either with resistance or susceptibility. Genetic mapping of these metabolites showed that a large number of them co-localize with whitefly-resistance QTLs. Some of these whitefly-resistance QTLs are hotspots for metabolite QTLs. Although a large number of metabolite QTLs correlated to whitefly resistance or susceptibility, most of them are yet unknown compounds and further studies are needed to identify the metabolic pathways and genes involved. The results indicate a direct genetic correlation between biochemical-based resistance characteristics and reduced whitefly incidence in S. pennellii.

Novel Genes Affecting the Interaction between the Cabbage Whitefly and Arabidopsis Uncovered by Genome-Wide Association Mapping

Plants have evolved a variety of ways to defend themselves against biotic attackers. This has resulted in the presence of substantial variation in defense mechanisms among plants, even within a species. Genome-wide association (GWA) mapping is a useful tool to study the genetic architecture of traits, but has so far only had limited exploitation in studies of plant defense. Here, we study the genetic architecture of defense against the phloem-feeding insect cabbage whitefly (Aleyrodes proletella) in Arabidopsis thaliana. We determined whitefly performance, i.e. the survival and reproduction of whitefly females, on 360 worldwide selected natural accessions and subsequently performed GWA mapping using 214,051 SNPs. Substantial variation for whitefly adult survival and oviposition rate (number of eggs laid per female per day) was observed between the accessions. We identified 39 candidate SNPs for either whitefly adult survival or oviposition rate, all with relatively small effects, underpinning the complex architecture of defense traits. Among the corresponding candidate genes, i.e. genes in linkage disequilibrium (LD) with candidate SNPs, none have previously been identified as a gene playing a role in the interaction between plants and phloem-feeding insects. Whitefly performance on knock-out mutants of a number of candidate genes was significantly affected, validating the potential of GWA mapping for novel gene discovery in plant-insect interactions. Our results show that GWA analysis is a very useful tool to gain insight into the genetic architecture of plant defense against herbivorous insects, i.e. we identified and validated several genes affecting whitefly performance that have not previously been related to plant defense against herbivorous insects.

Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum ‘Heinz’, an heirloom line, S. lycopersicum ‘Yellow Pear’, and two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato.

Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported.

Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.

Normal adult survival but reduced Bemisia tabaci oviposition rate on tomato lines carrying an introgression from S. habrochaites

Background

Host plant resistance has been proposed as one of the most promising approaches in whitefly management. Already in 1995 two quantitative trait loci (Tv-1 and Tv-2) originating from S. habrochaites CGN1.1561 were identified that reduced the oviposition rate of the greenhouse whitefly (Trialeurodes vaporariorum). After this first study, several others identified QTLs affecting whitefly biology as well. Generally, the QTLs affecting oviposition were highly correlated with a reduction in whitefly survival and the presence of high densities of glandular trichomes type IV. The aim of our study was to further characterize Tv-1 and Tv-2, and to determine their role in resistance against Bemisia tabaci.

Results

We selected F₂ plants homozygous for the Tv-1 and Tv-2 QTL regions and did three successive backcrosses without phenotypic selection. Twenty-three F₂BC₃ plants were phenotyped for whitefly resistance and differences were found in oviposition rate of B. tabaci. The F₂BC₃ plants with the lowest oviposition rate had an introgression on Chromosome 5 in common. Further F₂BC_4, F₂BC₄S₁ and F₂BC₄S₂ families were developed, genotyped and phenotyped for adult survival, oviposition rate and trichome type and density. It was possible to confirm that an introgression on top of Chr. 5 (OR-5), between the markers rs-2009 and rs-7551, was responsible for reducing whitefly oviposition rate.

Conclusion

We found a region of 3.06 Mbp at the top of Chr. 5 (OR-5) associated with a reduction in the oviposition rate of B. tabaci. This reduction was independent of the presence of the QTLs Tv-1 and Tv-2 as well as of the presence of trichomes type IV. The OR-5 locus will provide new opportunities for resistance breeding against whiteflies, which is especially relevant in greenhouse cultivation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0142-3) contains supplementary material, which is available to authorized users.

Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection

BACKGROUND

Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem development are known to regulate also fruit morphology. To decipher the genetic variation underlying tomato fruit morphology, we assessed the nucleotide diversity and selection footprints of candidate genes involved in flower and fruit development and performed genome-wide association studies.

RESULTS

Thirty candidate genes were selected according to their similarity with genes involved in meristem development or their known causal function in Arabidopsis thaliana. In tomato, these genes and flanking regions were sequenced in a core collection of 96 accessions (including cultivated, cherry-type and wild relative accessions) maximizing the molecular diversity, using the Roche 454 technology. A total amount of 17 Mb was sequenced allowing the discovery of 6,106 single nucleotide polymorphisms (SNPs). The annotation of the 30 gene regions identified 231 exons carrying 517 SNPs. Subsequently, the nucleotide diversity (π) and the neutral evolution of each region were compared against genome-wide values within the collection, using a SNP array carrying 7,667 SNPs mainly distributed in coding sequences.About half of the genes revealed footprints of selection and polymorphisms putatively involved in fruit size variation by showing negative Tajima's D and nucleotide diversity reduction in cultivated tomato compared to its wild relative. Among the candidates, FW2.2 and BAM1 sequences revealed selection footprints within their promoter regions suggesting their potential involvement in their regulation. Two associations co-localized with previously identified loci: LC (locule number) and Ovate (fruit shape).

CONCLUSION

Compared to whole genome genotypic data, a drastic reduction of nucleotide diversity was shown for several candidate genes. Strong selection patterns were identified in 15 candidates highlighting the critical role of meristem maintenance genes as well as the impact of domestication on candidates. The study highlighted a set of polymorphisms putatively important in the evolution of these genes.