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

New QTLs involved in the control of stigma position in tomato

BACKGROUND

Tomato mating systems were strongly affected by domestication events. Mutations disrupting self-incompatibility paralleled by changes retracting the stigma position (SP) within the staminal cone conferred strict autogamy and self-fertility to the cultivated forms. Although major genes affecting these changes have been identified, SP control in domesticated forms that retain a constitutive or heat-inducible noninserted SP needs elucidation. To widen the possibility of identifying SP genetic determinants, we analyzed the trait in four populations (two germplasm collections, a multiparental recombinant inbred and a biparental progeny) under different environmental conditions (normal and heat stressed).

RESULTS

Overall, 37 markers significantly associated with the trait were identified. Several colocalizations were found, both among regions first reported in this work and among them and previously reported positions. This finding supported the reliability of the analysis. Three such regions, in the long arms of chromosomes 1, 8 and 11, were validated in an independent segregating population, and candidate genes in confidence intervals were identified among transcription factors and hormone-, stress- and cell wall-related genes.

CONCLUSION

Overall, this work supported the hypothesis that the SP phenotype is controlled by different key genes in tomato, paving the way for the identification of novel players and novel mechanisms involved in the regulation of herkogamy.

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

GPA1 is a determinant of leaf width and fruit size in tomato

The identification and dissection of the genetic foundations underlying natural variations in crop species are critical for understanding their phenotypic diversity and for subsequent application in selective breeding. In this research, we identify a natural polymorphism in the promoter region of the G protein α subunit 1 (GPA1) gene, which is associated with the width of the tomato leaves. This may be an evolutionary consequence resulting from the domestication processes aimed at increasing fruit size. A functional disruption of the GPA1 gene resulted in a significant reduction in both the leaf size and the fruit mass in tomatoes compared to the wild type. Further exploration revealed that the intrinsic variation present in the GPA1 promoter region is responsible for the differential expression of the GPA1 gene. Distinct GPA1 haplotypes show a significant correlation with geographic distribution, suggesting that the polymorphisms within the GPA1 locus confer adaptive advantages for modulating leaf morphology in tomatoes, reflecting evolutionary responses to regional environmental pressures. Consequently, our findings provide new insights into the genetic diversity underlying leaf morphology and offer a valuable genetic resource for the selective breeding of cultivated tomato varieties.

Climate change-driven shifts in the global distribution of tomato and potato crops and their associated bacterial pathogens

Introduction

Climate change is increasingly affecting the global distribution and productivity of critical food crops, including Solanum lycopersicum (tomato) and Solanum tuberosum (potato). In particular, bacterial pathogens such as Clavibacter michiganensis and Ralstonia solanacearum are expected to shift their geographic ranges, posing new risks to these crops. This study hypothesizes that under future climate scenarios, the geographic overlap between these crops and their pathogens will increase in certain regions, leading to heightened agricultural risks, especially in areas currently considered safe from these pathogens.

Methods

To test our hypotheses, the objective was to evaluate the potential impact of climate change on the geographic distribution of two key food crops (tomato and potato) and their bacterial pathogens for the current time and by 2050. This study used four species distribution models (SDMs) to predict current and future habitat suitability for both tomato and potato crops, as well as their associated pathogens, under two shared socioeconomic pathways (SSP4.5 and SSP8.5) and four global circulation models (GCMs).

Results

The models projected significant poleward shifts in suitable habitats for tomatoes and potatoes, with notable expansions in higher-latitude regions such as Canada, northern Europe, and Russia, and contractions in current major production zones such as the United States (US), Brazil, parts of Africa, and China. For Clavibacter michiganensis, the overlap with tomatoes was substantial, whereas the overlap between potatoes and Ralstonia solanacearum was comparatively smaller.

Discussion

Our hypothesis was partially supported by the results. While the overall overlap between crop and pathogen habitats remains limited, the risk areas for both pathogens are expected to expand under future climate conditions in regions such as eastern Australia, Japan, Spain, and France. These findings underscore the importance of region-specific agricultural planning and pathogen management strategies to mitigate the risks posed by climate change. Future efforts should focus on vulnerable areas to prevent significant economic losses and ensure food security.

Identification of Cherry Tomato Volatiles Using Different Electron Ionization Energy Levels

A comprehensive analysis of the volatile components of 11 different cherry tomato pastes (Tesco Extra, Orange, Zebra, Yellow, Round Netherland, Mini San Marzano, Spar truss, Tesco Sunstream, Paprikakertész, Mc Dreamy, and Tesco Eat Fresh) commercially available in Hungary was performed. In order to ensure the reliability and accuracy of the measurement, the optimal measurement conditions were first determined. SPME (solid-phase microextraction) fiber coating, cherry tomato paste treatment, and SPME sampling time and temperature were optimized. CAR/PDMS (carboxen/polydimethylsiloxane) fiber coating with a film thickness of 85 µm is suggested at a 60 °C sampling temperature and 30 min extraction time. A total of 64 common compounds was found in the prepared, mashed cherry tomato samples, in which 59 compounds were successfully identified. Besides the already published compounds, new, cherry tomato-related compounds were found, such as 3 methyl 2 butenal, heptenal, Z-4-heptenal, E-2-heptenal, E-carveol, verbenol, limonene oxide, 2-decen-1-ol, Z-4-decen-1-al, caryophyllene oxide, and E,E-2,4-dodecadienal. Supervised and unsupervised classification methods have been used to classify the tomato varieties based on their volatiles, which identified 16 key components that enable the discrimination of the samples with a high accuracy.

The CELL NUMBER REGULATOR FW2.2 protein regulates cell-to-cell communication in tomato by modulating callose deposition at plasmodesmata

FW2.2 (standing for FRUIT WEIGHT 2.2), the founding member of the CELL NUMBER REGULATOR (CNR) gene family, was the first cloned gene underlying a quantitative trait locus (QTL) governing fruit size and weight in tomato (Solanum lycopersicum). However, despite this discovery over 20 yr ago, the molecular mechanisms by which FW2.2 negatively regulates cell division during fruit growth remain undeciphered. In the present study, we confirmed that FW2.2 is a membrane-anchored protein whose N- and C-terminal ends face the apoplast. We unexpectedly found that FW2.2 is located at plasmodesmata (PD). FW2.2 participates in the spatiotemporal regulation of callose deposition at PD and belongs to a protein complex which encompasses callose synthases. These results suggest that FW2.2 has a regulatory role in cell-to-cell communication by modulating PD transport capacity and trafficking of signaling molecules during fruit development.

Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum)

Micro-Tom is a cultivar of tomato (Solanum lycopersicum), which is known as a major crop and model plant in Solanaceae. Micro-Tom has phenotypic traits such as dwarfism, and substantial EMS-mutagenized lines have been reported. After Micro-Tom was generated in Florida, USA, it was distributed to research institutes worldwide and used as a genetic resource. In Japan, the Micro-Tom lines have been genetically fixed; currently, three lines have been re-distributed from three institutes, but many phenotypes among the lines have been observed. We have determined the genome sequence de novo of the Micro-Tom KDRI line, one of the Micro-Tom lines distributed from Kazusa DNA Research Institute (KDRI) in Japan, and have built chromosome-scale pseudomolecules. Genotypes among six Micro-Tom lines, including three in Japan, one in the United States, one in France, and one in Brazil showed phenotypic alternation. Here, we unveiled the swift emergence of genetic diversity in both phenotypes and genotypes within the Micro-Tom genome sequence during its propagation. These findings offer valuable insights crucial for the management of bioresources.

Rhizosphere Microbiome Co-Occurrence Network Analysis across a Tomato Domestication Gradient

When plant-available phosphorus (P) is lost from a soil solution, it often accumulates in the soil as a pool of unavailable legacy P. To acquire legacy P, plants employ recovery strategies, such as forming associations with soil microbes. However, the degree to which plants rely on microbial associations for this purpose varies with crop domestication and subsequent breeding. Here, by generating microbial co-occurrence networks, we sought to explore rhizosphere bacterial interactions in low-P conditions and how they change with tomato domestication and breeding. We grew wild tomato, traditional tomato (developed circa 1900), and modern tomato (developed circa 2020) in high-P and low-P soil throughout their vegetative developmental stage. Co-occurrence network analysis revealed that as the tomatoes progressed along the stages of domestication, the rhizosphere microbiome increased in complexity in a P deficit. However, with the addition of P fertilizer, the wild tomato group became more complex, surpassing the complexity of traditional and modern tomato, suggesting a high degree of responsiveness in the rhizosphere microbiome to P fertilizer by wild tomato relatives. By illustrating these changing patterns of network complexity in the tomato rhizosphere microbiome, we can further understand how plant domestication and breeding have shaped plant-microbe interactions.

A novel tomato interspecific (Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm

We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.

Inhibition Mechanism of Water-Soluble Chitosan-Curdlan Composite Coating on the Postharvest Pathogens of Serratia marcescens and Pseudomonas syringae in Cherry Tomatoes

Cherry tomatoes, a very popular fruit, are highly susceptible to microbial infestation, which cause significant economic losses. In order to preserve cherry tomatoes better, we treat them with a Chitosan (CTS) and Curdlan (CUR) composite coating. The lowest inhibitory concentration of CTS/CUR composite coating on Serratia marcescens and Pseudomonas syringae, the growth curves, and the changes of the cell lysis rate were determined to explore the inhibitory mechanism of CTS/CUR composite coating on Serratia marcescens and Pseudomonas syringae and the microscopic morphology of Serratia marcescens and Pseudomonas syringae was observed using scanning electron microscopy at the same time. The results showed that the CTS/CUR composite coating could effectively inhibit the growth of Serratia marcescens and Pseudomonas, and the inhibitory effect reflected the concentration-dependent characteristics. The electron microscopy results indicated that the inhibition of Serratia marcescens and Pseudomonas syringae by the CTS/CUR composite coating might originate from its disruptive effect on the cell wall and cell membrane of the bacterium.

Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding

Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.

Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions

Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Interspecific hybridization, a widely employed technique in tomato breeding, results in the creation of novel combinations of TEs from distinct species. The implications of this process for TE transposition activity have not been studied in modern cultivars. In this study, we used nanopore sequencing of extrachromosomal circular DNA (eccDNA) and identified two highly active Ty1/Copia LTR retrotransposon families of tomato (Solanum lycopersicum), called Salsa and Ketchup. Elements of these families produce thousands of eccDNAs under controlled conditions and epigenetic stress. EccDNA sequence analysis revealed that the major parts of eccDNA produced by Ketchup and Salsa exhibited low similarity to the S. lycopersicum genomic sequence. To trace the origin of these TEs, whole-genome nanopore sequencing and de novo genome assembly were performed. We found that these TEs occurred in a tomato breeding line via interspecific introgression from S. peruvianum. Our findings collectively show that interspecific introgressions can contribute to both genetic and phenotypic diversity not only by introducing novel genetic variants, but also by importing active transposable elements from other species.

A natural variation in SlSCaBP8 promoter contributes to the loss of saline-alkaline tolerance during tomato improvement

Saline-alkaline stress is a worldwide problem that threatens the growth and yield of crops. However, how crops adapt to saline-alkaline stress remains less studied. Here we show that saline-alkaline tolerance was compromised during tomato domestication and improvement, and a natural variation in the promoter of SlSCaBP8, an EF-hand Ca2+ binding protein, contributed to the loss of saline-alkaline tolerance during tomato improvement. The biochemical and genetic data showed that SlSCaBP8 is a positive regulator of saline-alkaline tolerance in tomato. The introgression line Pi-75, derived from a cross between wild Solanum pimpinellifolium LA1589 and cultivar E6203, containing the SlSCaBP8LA1589 locus, showed stronger saline-alkaline tolerance than E6203. Pi-75 and LA1589 also showed enhanced saline-alkaline-induced SlSCaBP8 expression than that of E6203. By sequence analysis, a natural variation was found in the promoter of SlSCaBP8 and the accessions with the wild haplotype showed enhanced saline-alkaline tolerance compared with the cultivar haplotype. Our studies clarify the mechanism of saline-alkaline tolerance conferred by SlSCaBP8 and provide an important natural variation in the promoter of SlSCaBP8 for tomato breeding.

Recent Advances in Tomato Gene Editing

The use of gene-editing tools, such as zinc finger nucleases, TALEN, and CRISPR/Cas, allows for the modification of physiological, morphological, and other characteristics in a wide range of crops to mitigate the negative effects of stress caused by anthropogenic climate change or biotic stresses. Importantly, these tools have the potential to improve crop resilience and increase yields in response to challenging environmental conditions. This review provides an overview of gene-editing techniques used in plants, focusing on the cultivated tomatoes. Several dozen genes that have been successfully edited with the CRISPR/Cas system were selected for inclusion to illustrate the possibilities of this technology in improving fruit yield and quality, tolerance to pathogens, or responses to drought and soil salinity, among other factors. Examples are also given of how the domestication of wild species can be accelerated using CRISPR/Cas to generate new crops that are better adapted to the new climatic situation or suited to use in indoor agriculture.

Endophytic biofungicide Bacillus subtilis (NBRI-W9) reshapes the metabolic homeostasis disrupted by the chemical fungicide, propiconazole in tomato plants to provide sustainable immunity against non-target bacterial pathogens

Chemical and microbial fungicides (Bio/fungicide) act differentially on plant systems. The present work assessed the metabolic profile of tomato plants vis-a-vis endophytic diversity after spraying of Propiconazole (PCZ) and endophytic biofungicide Bacillus subtilis (W9). Bio/fungicides were sprayed on tomato plants and evaluated for phenotypic, biochemical, and metabolic profiles after one week. In W9 treatment, a significant increase in relative abundance of several metabolites was observed including sugars, sugar alcohols, fatty-acids, organic-acids, and amino-acids. Polysaccharides and fatty acids showed a significant positive correlation with Rhizobiales, Burkholderiales, Bacillales, and Lactobacillales, respectively (p < 0.05). The PCZ and W9 treated plant's metabolic status significantly affected their resistance to non-target, bacterial pathogen P. syringae. Compared to PCZ and control, W9 treatment reduced the ROS deposition and expression of antioxidants gene GPx, PO (~0.1-1.7fold). It enhanced the genes related to the Phenylpropanoid pathway (∼1.6-5.2 fold), PR protein (~1.2-3.4 fold), and JA biosynthesis (~1.7-4.3 fold), resulting in reduced disease incidence. The results provide novel insights into the effects of endophytic biofungicide and chemical fungicides on the plant's metabolic status, its relation to the endophytes, and role in altering the plant's immune system.

Detection of trait donors and QTL boundaries for early blight resistance using local ancestry inference in a library of genomic sequences for tomato

By conducting hierarchical clustering along a sliding window, we generated haplotypes across hundreds of re-sequenced genomes in a few hours. We leveraged our method to define cryptic introgressions underlying disease resistance in tomato (Solanum lycopersicum L.) and to discover resistant germplasm in the tomato seed bank. The genomes of 9 accessions with early blight (Alternaria linariae) disease resistance were newly sequenced and analyzed together with published sequences for 770 tomato and wild species accessions, most of which are available in germplasm collections. Identification of common ancestral haplotypes among resistant germplasm enabled rapid fine mapping of recently discovered quantitative trait loci (QTL) conferring resistance and the identification of possible causal variants. The source of the early blight QTL EB-9 was traced to a vintage tomato named 'Devon Surprise'. Another QTL, EB-5, as well as resistance to bacterial spot disease (Xanthomonas spp.), was traced to Hawaii 7998. A genomic survey of all accessions forecasted EB-9-derived resistance in several heirloom tomatoes, accessions of S. lycopersicum var. cerasiforme, and S. pimpinellifolium PI 37009. Our haplotype-based predictions were validated by screening the accessions against the causal pathogen. There was little evidence of EB-5 prevalence in surveyed contemporary germplasm, presenting an opportunity to bolster tomato disease resistance by adding this rare locus. Our work demonstrates practical insights that can be derived from the efficient processing of large genome-scale datasets, including rapid functional prediction of disease resistance QTL in diverse genetic backgrounds. Finally, our work finds more efficient ways to leverage public genetic resources for crop improvement.

Plant Variety, Mycorrhization, and Herbivory Influence Induced Volatile Emissions and Plant Growth Characteristics in Tomato

Plants produce a range of volatile organic compounds (VOCs) that mediate vital ecological interactions between herbivorous insects, their natural enemies, plants, and soil dwelling organisms including arbuscular mycorrhizal fungi (AMF). The composition, quantity, and quality of the emitted VOCs can vary and is influenced by numerous factors such as plant species, variety (cultivar), plant developmental stage, root colonization by soil microbes, as well as the insect developmental stage, and level of specialization of the attacking herbivore. Understanding factors shaping VOC emissions is important and can be leveraged to enhance plant health and pest resistance. In this greenhouse study, we evaluated the influence of plant variety, mycorrhizal colonization, herbivory, and their interactions on the composition of emitted volatiles in tomato plants (Solanum lycopersicum L.). Four tomato varieties from two breeding histories (two heirlooms and two hybrids), were used. Tomato plants were inoculated with a commercial inoculum blend consisting of four species of AMF. Plants were also subjected to herbivory by Manduca sexta (Lepidoptera: Sphingidae L.) five weeks after transplanting. Headspace volatiles were collected from inoculated and non-inoculated plants with and without herbivores using solid phase-microextraction. Volatile profiles consisted of 21 different volatiles in detectable quantities. These included monoterpenes, sesquiterpenes, and alkane hydrocarbons. We documented a strong plant variety effect on VOC emissions. AMF colonization and herbivory suppressed VOC emissions. Plant biomass was improved by colonization of AMF. Our results show that mycorrhization, herbivory and plant variety can alter tomato plant VOC emissions and further shape volatile-mediated insect and plant interactions.

Engineering homoeologs provide a fine scale for quantitative traits in polyploid

Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR-Cas9-mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad-spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops.

Form and contour: breeding and genetics of organ shape from wild relatives to modern vegetable crops

Shape is a primary determinant of consumer preference for many horticultural crops and it is also associated with many aspects of marketing, harvest mechanics, and postharvest handling. Perceptions of quality and preference often map to specific shapes of fruits, tubers, leaves, flowers, roots, and other plant organs. As a result, humans have greatly expanded the palette of shapes available for horticultural crops, in many cases creating a series of market classes where particular shapes predominate. Crop wild relatives possess organs shaped by natural selection, while domesticated species possess organs shaped by human desires. Selection for visually-pleasing shapes in vegetable crops resulted from a number of opportunistic factors, including modification of supernumerary cambia, allelic variation at loci that control fundamental processes such as cell division, cell elongation, transposon-mediated variation, and partitioning of photosynthate. Genes that control cell division patterning may be universal shape regulators in horticultural crops, influencing the form of fruits, tubers, and grains in disparate species. Crop wild relatives are often considered less relevant for modern breeding efforts when it comes to characteristics such as shape, however this view may be unnecessarily limiting. Useful allelic variation in wild species may not have been examined or exploited with respect to shape modifications, and newly emergent information on key genes and proteins may provide additional opportunities to regulate the form and contour of vegetable crops.

Genomic basis of selective breeding from the closest wild relative of large-fruited tomato

The long and intricate domestication history of the tomato (Solanum lycopersicum) includes selection sweeps that have not been fully explored, and these sweeps show significant evolutionary trajectories of domestication traits. Using three distinct selection strategies, we represented comprehensive selected sweeps from 53 Solanum pimpinellifolium (PIM) and 166 S. lycopersicum (BIG) accessions, which are defined as pseudo-domestication in this study. We identified 390 potential selection sweeps, some of which had a significant impact on fruit-related traits and were crucial to the pseudo-domestication process. During tomato pseudo-domestication, we discovered a minor-effect allele of the SlLEA gene related to fruit weight (FW), as well as the major haplotypes of fw2.2/cell number regulator (CNR), fw3.2/SlKLUH, and fw11.3/cell size regulator (CSR) in cultivars. Furthermore, 18 loci were found to be significantly associated with FW and six fruit-related agronomic traits in genome-wide association studies. By examining population differentiation, we identified the causative variation underlying the divergence of fruit flavonoids across the large-fruited tomatoes and validated BRI1-EMS-SUPPRESSOR 1.2 (SlBES1.2), a gene that may affect flavonoid content by modulating the MYB12 expression profile. Our results provide new research routes for the genetic basis of fruit traits and excellent genomic resources for tomato genomics-assisted breeding.

An Integrative Transcriptomics and Proteomics Approach to Identify Putative Genes Underlying Fruit Ripening in Tomato near Isogenic Lines with Long Shelf Life

The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.

Feeding the world: impacts of elevated [CO2] on nutrient content of greenhouse grown fruit crops and options for future yield gains

Several long-term studies have provided strong support demonstrating that growing crops under elevated [CO2] can increase photosynthesis and result in an increase in yield, flavour and nutritional content (including but not limited to Vitamins C, E and pro-vitamin A). In the case of tomato, increases in yield by as much as 80% are observed when plants are cultivated at 1000 ppm [CO2], which is consistent with current commercial greenhouse production methods in the tomato fruit industry. These results provide a clear demonstration of the potential for elevating [CO2] for improving yield and quality in greenhouse crops. The major focus of this review is to bring together 50 years of observations evaluating the impact of elevated [CO2] on fruit yield and fruit nutritional quality. In the final section, we consider the need to engineer improvements to photosynthesis and nitrogen assimilation to allow plants to take greater advantage of elevated CO2 growth conditions.

Reference Guided De Novo Genome Assembly of Transformation Pliable Solanum lycopersicum cv. Pusa Ruby

Solanum lycopersicum cv. Pusa Ruby (PR) is a superior tomato cultivar routinely used as a model tomato variety. Here, we report a reference-guided genome assembly for PR, covering 97.6% of the total single-copy genes in the solanales order. The PR genome contains 34,075 genes and 423,288 variants, out of which 127,131 are intragenic and 1232 are of high impact. The assembly was packaged according to PanSol guidelines (N50 = 60,396,827) with the largest scaffold measuring 85 megabases. The similarity of the PR genome assembly to Heinz1706, M82, and Fla.8924 was measured and the results suggest PR has the lowest affinity towards the hybrid Fla.8924. We then analyzed the regeneration efficiency of PR in comparison to another variety, Pusa Early Dwarf (PED). PR was found to have a high regeneration rate (45.51%) and therefore, we performed allele mining for genes associated with regeneration and found that only AGAMOUS-LIKE15 has a null mutation. Further, allele mining for fruit quality-related genes was also executed. The PR genome has an Ovate mutation leading to round fruit shape, causing economically undesirable fruit cracking. This genomic data can be potentially used for large scale crop improvement programs as well as functional annotation studies.

Plasticity of maternal environment-dependent expression-QTLs of tomato seeds

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depend on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to construct a linkage map and measure gene expression of seeds of a tomato recombinant inbred line (RIL) population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments, i.e., on high phosphorus or low nitrogen. The obtained single-nucleotide polymorphisms (SNPs) were subsequently used to construct a genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

Antioxidant and Anti-Inflammatory Compounds from Edible Plants with Anti-Cancer Activity and Their Potential Use as Drugs

Food is our daily companion, performing numerous beneficial functions for our bodies. Many of them can help to alleviate or prevent ailments and diseases. In this review, an extensive bibliographic search is conducted in various databases to update information on unprocessed foods with anti-inflammatory and antioxidant properties that can aid in treating diseases such as cancer. The current state of knowledge on inflammatory processes involving some interleukins and tumor necrosis factor-alpha (TNF-α) is reviewed. As well as unprocessed foods, which may help reduce inflammation and oxidative stress, both of which are important factors in cancer development. Many studies are still needed to take full advantage of the food products we use daily.

Genetic analysis of the tomato russet mite provides evidence of oligophagy and a widespread pestiferous haplotype

Worldwide, the tomato russet mite (TRM), Aculops lycopersici (Eriophyidae), is a key pest on cultivated tomato in addition to infesting other cultivated and wild Solanaceae; however, basic information on TRM supporting effective control strategies is still lacking, mainly regarding its taxonomic status and genetic diversity and structure. As A. lycopersici is reported on different species and genera of host plants, populations associated with different host plants may constitute specialized cryptic species, as shown for other eriophyids previously considered generalists. The main aims of this study were to (i) confirm the TRM taxonomic unity of populations from different host plants and localities as well as the species' oligophagy, and (ii) to advance the understanding of TRM host relationship and invasion history. For this purpose, we evaluated the genetic variability and structure of populations from different host plants along crucial areas of occurrence, including the area of potential origin, based on DNA sequences of mitochondrial (cytochrome c oxidase subunit I) and nuclear (internal transcribed spacer, D2 28S) genomic regions. Specimens from South America (Brazil) and Europe (France, Italy, Poland, The Netherlands) were collected from tomato and other solanaceous species from the genera Solanum and Physalis. Final TRM datasets were composed of 101, 82 and 50 sequences from the COI (672 bp), ITS (553 bp) and D2 (605 bp) regions, respectively. Distributions and frequencies of haplotypes (COI) and genotypes (D2 and ITS1) were inferred; pairwise genetic distance comparisons, and phylogenetic analysis were performed, including Bayesian Inference (BI) combined analysis. Our results showed that genetic divergences for mitochondrial and nuclear genomic regions from TRM associated with different host plants were lower than those observed in other eriophyid taxa, confirming conspecificity of TRM populations and oligophagy of this eriophyid mite. Four haplotypes (cH) were identified from the COI sequences with cH1 being the most frequent, representing 90% of all sequences occurring in all host plants studied (Brazil, France, The Netherlands); the other haplotypes were present exclusively in Brazilian populations. Six variants (I) were identified from the ITS sequences: I-1 was the most frequent (76.5% of all sequences), spread in all countries and associated with all host plants, except S. nigrum. Just one D2 sequence variant was found in all studied countries. The genetic homogeneity among populations highlights the occurrence of a highly invasive and oligophagous haplotype. These results failed to corroborate the hypothesis that differential symptomatology or damage intensity among tomato varieties and solanaceous host plants could be due to the genetic diversity of the associated mite populations. The genetic evidence, along with the history of spread of cultivated tomato, corroborates the hypothesis of a South American origin of TRM.

Genetic architecture of fresh-market tomato yield

BACKGROUND

The fresh-market tomato (Solanum lycopersicum) is bred for direct consumption and is selected for a high yield of large fruits. To understand the genetic variations (distinct types of DNA sequence polymorphism) that influence the yield, we collected the phenotypic variations in the yields of total fruit, extra-large-sized fruit, small-sized fruit, or red-colored fruit from 68 core inbred contemporary U.S. fresh-market tomatoes for three consecutive years and the genomic information in 8,289,741 single nucleotide polymorphism (SNP) positions from the whole-genome resequencing of these tomatoes.

RESULTS

Genome-wide association (GWA) mapping using the SNP data with or without SNP filtering steps using the regularization methods, validated with quantitative trait loci (QTL) linkage mapping, identified 18 significant association signals for traits evaluated. Among them, 10 of which were not located within genomic regions previously identified as being associated with fruit size/shape. When mapping-driven association signals [558 SNPs associated with 28 yield (component) traits] were used to calculate genomic estimated breeding values (GEBVs) of evaluated traits, the prediction accuracies of the extra-large-sized fruit and small-sized fruit yields were higher than those of the total and red-colored fruit yields, as we tested the generated breeding values in inbred tomatoes and F2 populations. Improved accuracy in GEBV calculation of evaluated traits was achieved by using 364 SNPs identified using the regularization methods.

CONCLUSIONS

Together, these results provide an understanding of the genetic variations underlying the heritable phenotypic variability in yield in contemporary tomato breeding and the information necessary for improving such economically important and complex quantitative trait through breeding.

Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis

Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.

Food security and the cultural heritage missing link

Though enormous strides have been achieved in recent decades towards reducing food insecurity in the Global South, continued efforts are imperative in light of rapidly expanding populations and threats posed by climate change. A relatively unexplored area in this arena is the nexus between cultural heritage and food security. Cultural heritage embodies indigenous culture, values, and traditions inherited from previous generations. We focus on rice and identify five pathways through which cultural heritage affects food security. Although policy makers face the complex task of balancing trade-offs between preserving cultural heritage and productivity, they can harness cultural heritage to enhance food security by supporting (i) preservation of genetic resources, (ii) valorization, (iii) traditional food processing, (iv) preference matching, and (v) agritourism.

Multispecies transcriptomes reveal core fruit development genes

During angiosperm evolution there have been repeated transitions from an ancestral dry fruit to a derived fleshy fruit, often with dramatic ecological and economic consequences. Following the transition to fleshy fruits, domestication may also dramatically alter the fruit phenotype via artificial selection. Although the morphologies of these fruits are well documented, relatively less is known about the molecular basis of these developmental and evolutionary shifts. We generated RNA-seq libraries from pericarp tissue of desert tobacco and both cultivated and wild tomato species at common developmental time points and combined this with corresponding, publicly available data from Arabidopsis and melon. With this broadly sampled dataset consisting of dry/fleshy fruits and wild/domesticated species, we applied novel bioinformatic methods to investigate conserved and divergent patterns of gene expression during fruit development and evolution. A small set of 121 orthologous "core" fruit development genes show a common pattern of expression across all five species. These include key players in developmental patterning such as orthologs of KNOLLE, PERIANTHIA, and ARGONAUTE7. GO term enrichment suggests that these genes function in basic cell division processes, cell wall biosynthesis, and developmental patterning. We furthermore uncovered a number of "accessory" genes with conserved expression patterns within but not among fruit types, and whose functional enrichment highlights the conspicuous differences between these phenotypic classes. We observe striking conservation of gene expression patterns despite large evolutionary distances, and dramatic phenotypic shifts, suggesting a conserved function for a small subset of core fruit development genes.

Next generation sequencing technologies to explore the diversity of germplasm resources: achievements and trends in tomato

Tomato is one of the major vegetable crops grown worldwide and a model species for genetic and biological research. Progress in genomic technologies made possible the development of forefront methods for high-scale sequencing, providing comprehensive insight into the genetic architecture of germplasm resources. This review revisits next-generation sequencing strategies and applications to investigate the diversity of tomato, describing the common platforms used for SNP genotyping of large collections, de novo sequencing, and whole genome resequencing. Significant findings in evolutionary history are outlined, thus discussing how genomics has provided new hints about the processes behind domestication. Finally, achievement and perspectives on pan-genome construction and graphical pan-genome development toward precise mining of the natural variation to be exploited for breeding purposes are presented.

Tomato Leaf Disease Recognition on Leaf Images Based on Fine-Tuned Residual Neural Networks

Humans depend heavily on agriculture, which is the main source of prosperity. The various plant diseases that farmers must contend with have constituted a lot of challenges in crop production. The main issues that should be taken into account for maximizing productivity are the recognition and prevention of plant diseases. Early diagnosis of plant disease is essential for maximizing the level of agricultural yield as well as saving costs and reducing crop loss. In addition, the computerization of the whole process makes it simple for implementation. In this paper, an intelligent method based on deep learning is presented to recognize nine common tomato diseases. To this end, a residual neural network algorithm is presented to recognize tomato diseases. This research is carried out on four levels of diversity including depth size, discriminative learning rates, training and validation data split ratios, and batch sizes. For the experimental analysis, five network depths are used to measure the accuracy of the network. Based on the experimental results, the proposed method achieved the highest F1 score of 99.5%, which outperformed most previous competing methods in tomato leaf disease recognition. Further testing of our method on the Flavia leaf image dataset resulted in a 99.23% F1 score. However, the method had a drawback that some of the false predictions were of tomato early light and tomato late blight, which are two classes of fine-grained distinction.

Variation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip

The domestication of tomato has led to striking variations in fruit morphology. Here, we show a genome-wide association study (GWAS) to understand the development of the fruit tip and describe a POINTED TIP (PT) gene that encodes a C2H2-type zinc finger transcription factor. A single nucleotide polymorphism is found to change a histidine (H) to an arginine (R) in the C2H2 domain of PT and the two alleles are referred to as PT^H and PT^R. Knocking out PT^H leads to development of pointed tip fruit. PT^H functions to suppress pointed tip formation by downregulating the transcription of FRUTFULL 2 (FUL2), which alters the auxin transport. Our evolutionary analysis and previous studies by others suggest that the PT^R allele likely hitch-hiked along with other selected loci during the domestication process. This study uncovers variation in PT and molecular mechanism underlying fruit tip development in tomato.

While auxin has been implicated in the development of tomato fruit with pointed tips, the mechanism are largely unknown. Here, the authors report variation of a C2H2-type zinc finger transcription factor affects transcription of FUL2, which consequently regulates auxin transport and distribution to determine tomato fruit shape.

Increased ACS Enzyme Dosage Causes Initiation of Climacteric Ethylene Production in Tomato

Fruits of wild tomato species show different ethylene-dependent ripening characteristics, such as variations in fruit color and whether they exhibit a climacteric or nonclimacteric ripening transition. 1-Aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC oxidase (ACO) are key enzymes in the ethylene biosynthetic pathway encoded by multigene families. Gene duplication is a primary driver of plant diversification and angiosperm evolution. Here, interspecific variations in the molecular regulation of ethylene biosynthesis and perception during fruit ripening in domesticated and wild tomatoes were investigated. Results showed that the activated ACS genes were increased in number in red-ripe tomato fruits than in green-ripe tomato fruits; therefore, elevated dosage of ACS enzyme promoted ripening ethylene production. Results showed that the expression of three ACS isogenes ACS1A, ACS2, and ACS4, which are involved in autocatalytic ethylene production, was higher in red-ripe tomato fruits than in green-ripe tomato fruits. Elevated ACS enzyme dosage promoted ethylene production, which corresponded to the climacteric response of red-ripe tomato fruits. The data suggest that autoinhibitory ethylene production is common to all tomato species, while autocatalytic ethylene production is specific to red-ripe species. The essential regulators Non-ripening (NOR) and Ripening-Inhibitor (RIN) have experienced gene activation and overlapped with increasing ACS enzyme dosage. These complex levels of transcript regulation link higher ethylene production with spatiotemporal modulation of gene expression in red-ripe tomato species. Taken together, this study shows that bursts in ethylene production that accompany fruit color changes in red-ripe tomatoes are likely to be an evolutionary adaptation for seed dispersal.

Characterizing rhizosphere microbial communities associated with tolerance to aboveground herbivory in wild and domesticated tomatoes

Root-associated microbial communities are well known for their ability to prime and augment plant defenses that reduce herbivore survival or alter behavior (i.e., resistance). In contrast, the role root microbes play in plant tolerance to herbivory, an evolutionarily sustainable alternative to resistance, is overlooked. In this study, we aimed to expand our limited understanding of what role rhizosphere microbial communities play in supporting tolerance to insect damage. Using domesticated tomatoes and their wild ancestors (Solanum spp.), we first documented how tobacco hornworm (Manduca sexta) herbivory impacted tomato fruit production in order to quantify plant tolerance. We then characterized the bacterial and fungal rhizosphere communities harbored by high and low tolerance plants. Wild tomatoes excelled at tolerating hornworm herbivory, experiencing no significant yield loss despite 50% leaf area removal. Their domesticated counterparts, on the other hand, suffered 26% yield losses under hornworm herbivory, indicating low tolerance. Ontogeny (i.e., mid- vs. late-season sampling) explained the most variation in rhizosphere community structure, with tomato line, tolerance, and domestication status also shaping rhizosphere communities. Fungal and bacterial community traits that associated with the high tolerance line include (1) high species richness, (2) relatively stable community composition under herbivory, and (3) the relative abundance of taxa belonging to Stenotrophomonas, Sphingobacterium, and Sphingomonas. Characterizing tolerance-associating microbiomes may open new avenues through which plant defenses are amended in pest management, such as plant breeding efforts that enhance crop recruitment of beneficial microbiomes.

Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (Solanum lycopersicum L.)

The western part of South America is a centre of diversity for tomatoes, but genetic diversity studies are lacking for parts of that region, including Bolivia. We used 11 simple sequence repeat (SSR) markers (including seven novel markers) to evaluate genetic diversity and population structure of 28 accessions (four modern cultivars, four advanced lines, nine landraces, 11 wild populations), and to compare their genetic variation against phenotypic traits, geographical origin and altitude. In total, 33 alleles were detected across all loci, with 2-5 alleles per locus. The top three informative SSRs were SLM6-11, LE20592 and TomSatX11-1, with polymorphism information content (PIC) of 0.65, 0.55 and 0.49, respectively. The genetic diversity of Bolivian tomatoes was low, as shown by mean expected heterozygosity (He) of 0.07. Analysis of molecular variance (AMOVA) revealed that 77.3% of the total variation was due to variation between accessions. Significant genetic differentiation was found for geographical origin, cultivation status, fruit shape, fruit size and growth type, each explaining 16-23% of the total variation. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree and principal coordinate analysis (PCoA) scatter plot both revealed differentiation between accessions with determinate flowers and accessions with indeterminate flowers, regardless of cultivation status. The genetic profiles of the accessions suggest that the Bolivian tomato gene pool comprises both strictly self-pollinating and open-pollinating genotypes.

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.

Flavor and Other Quality Traits of Tomato Cultivars Bred for Diverse Production Systems as Revealed in Organic Low-Input Management

This study was conducted to determine the volatile organic compounds (VOCs) associated with fruit flavor in diverse tomato cultivars (salad and cocktail cultivars) under organic low-input production. For this objective, 60 cultivars deriving from very diverse breeding programs 1880-2015 were evaluated in 2015, and a subset of 20 cultivars was selected for further evaluation in 2016. The diversity of instrumentally determined traits, especially for VOCs concentration and sensory properties (fruit firmness, juiciness, skin firmness, sweetness, sourness, aroma, and acceptability), was investigated at two harvest dates. The evaluation of the cultivars exhibited a wide range of variation for all studied traits, with the exception of a few VOCs. Cultivar had the most important effect on all instrumentally determined traits, while the influence of cultivar × harvest date × year interaction was significant for 17 VOCs, but not for total soluble solid (TSS) and titratable acidity (TA). The VOCs with the highest proportion (>8%) were hexanal, 6-methyl-5-heptene-2-one, 2-isobutylthiazole, and (E)-2-hexenal, which were identified in all cultivars. Twelve VOCs significantly correlated with one or more sensory attributes and these VOCs also allowed differentiation of the fruit type. Among these VOCs, phenylethyl alcohol and benzyl alcohol positively correlated with acceptability in the cocktail cultivars, whereas 2-isobuthylthiazole and 6-methyl-5-hepten-2-ol negatively correlated with acceptability in the salad cultivars. As a result of this study, organic breeders are recommended to use cultivars from a wide range of breeding programs to improve important quality and agronomic traits. As examples, salad tomatoes "Campari F1", "Green Zebra", and "Auriga", as well as cocktail tomatoes "Supersweet 100 F1", "Sakura F1", and "Black Cherry" showed higher scores for the sensory attributes aroma and acceptability under organic low-input growing conditions. It remains a challenge for breeders and growers to reduce the trade-off of yield and quality.

Newly Discovered Alleles of the Tomato Antiflorigen Gene SELF PRUNING Provide a Range of Plant Compactness and Yield

In tomato cultivation, a rare natural mutation in the flowering repressor antiflorigen gene SELF-PRUNING (sp-classic) induces precocious shoot termination and is the foundation in determinate tomato breeding for open field production. Heterozygous single flower truss (sft) mutants in the florigen SFT gene in the background of sp-classic provide a heterosis-like effect by delaying shoot termination, suggesting the subtle suppression of determinacy by genetic modification of the florigen–antiflorigen balance could improve yield. Here, we isolated three new sp alleles from the tomato germplasm that show modified determinate growth compared to sp-classic, including one allele that mimics the effect of sft heterozygosity. Two deletion alleles eliminated functional transcripts and showed similar shoot termination, determinate growth, and yields as sp-classic. In contrast, amino acid substitution allele sp-5732 showed semi-determinate growth with more leaves and sympodial shoots on all shoots. This translated to greater yield compared to the other stronger alleles by up to 42%. Transcriptome profiling of axillary (sympodial) shoot meristems (SYM) from sp-classic and wild type plants revealed six mis-regulated genes related to the floral transition, which were used as biomarkers to show that the maturation of SYMs in the weaker sp-5732 genotype is delayed compared to sp-classic, consistent with delayed shoot termination and semi-determinate growth. Assessing sp allele frequencies from over 500 accessions indicated that one of the strong sp alleles (sp-2798) arose in early breeding cultivars but was not selected. The newly discovered sp alleles are potentially valuable resources to quantitatively manipulate shoot growth and yield in determinate breeding programs, with sp-5732 providing an opportunity to develop semi-determinate field varieties with higher yields.

European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci

A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent secondary centers of diversity with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a genome-wide association study with fruit morphological traits in the European traditional collection. The corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise a low-diversity population suggests a history of balancing selection, in which tomato farmers likely maintained the morphological variation by inadvertently applying a high selective pressure within different varietal types.

Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication

Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.

A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.

Electroantennogram and machine learning reveal a volatile blend mediating avoidance behavior by Tuta absoluta females to a wild tomato plant

Tomato cultivation is threatened by the infestation of the nocturnal invasive tomato pinworm, Tuta absoluta. This study was based on field observations that a wild tomato plant, Solanum lycopersicum var. cerasiforme, grown in the Mount Kenya region, Kenya, is less attacked by T. absoluta, unlike the cultivated tomato plants like S. lycopersicum (var. Rambo F1). We hypothesized that the wild tomato plant may be actively avoided by gravid T. absoluta females because of the emission of repellent allelochemical constituents. Therefore, we compared infestation levels by the pest in field monocrops and intercrops of the two tomato genotypes, characterized the headspace volatiles, then determined the compounds detectable by the insect through gas chromatography-linked electroantennography (GC-EAG), and finally performed bioassays using a blend of four EAG-active compounds unique to the wild tomato. We found significant reductions in infestation levels in the monocrop of the wild tomato, and intercrops of wild and cultivated tomato plants compared to the monocrop of the cultivated tomato plant. Quantitative and qualitative differences were noted between volatiles of the wild and cultivated tomato plants, and between day and night volatile collections. The most discriminating compounds between the volatile treatments varied with the variable selection or machine learning methods used. In GC-EAG recordings, 16 compounds including hexanal, (Z)-3-hexenol, α-pinene, β-myrcene, α-phellandrene, β-phellandrene, (E)-β-ocimene, terpinolene, limonene oxide, camphor, citronellal, methyl salicylate, (E)-β-caryophyllene, and others tentatively identified as 3,7,7-Trimethyl-1,3,5-cycloheptatriene, germacrene D and cis-carvenone oxide were detected by antennae of T. absoluta females. Among these EAG-active compounds, (Z)-3-hexenol, α-pinene, α-phellandrene, limonene oxide, camphor, citronellal, (E)-β-caryophyllene and β-phellandrene are in the top 5 discriminating compounds highlighted by the machine learning methods. A blend of (Z)-3-hexenol, camphor, citronellal and limonene oxide detected only in the wild tomato showed dose-dependent repellence to T. absoluta females in wind tunnel. This study provides some groundwork for exploiting the allelochemicals of the wild tomato in the development of novel integrated pest management approaches against T. absoluta.

Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato

The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.

Leveraging a graft collection to develop metabolome-based trait prediction for the selection of tomato rootstocks with enhanced salt tolerance

Grafting has been demonstrated to significantly enhance the salt tolerance of crops. However, breeding efforts to develop enhanced graft combinations are hindered by knowledge-gaps as to how rootstocks mediate scion-response to salt stress. We grafted the scion of cultivated M82 onto rootstocks of 254 tomato accessions and explored the morphological and metabolic responses of grafts under saline conditions (EC = 20 dS m^-1) as compared to self-grafted M82 (SG-M82). Correlation analysis and Least Absolute Shrinkage and Selection Operator were performed to address the association between morphological diversification and metabolic perturbation. We demonstrate that grafting the same variety onto different rootstocks resulted in scion phenotypic heterogeneity and emphasized the productivity efficiency of M82 irrespective of the rootstock. Spectrophotometric analysis to test lipid oxidation showed largest variability of malondialdehyde (MDA) equivalents across the population, while the least responsive trait was the ratio of fruit fresh weight to total fresh weight (FFW/TFW). Generally, grafts showed greater values for the traits measured than SG-M82, except for branch number and wild race-originated rootstocks; the latter were associated with smaller scion growth parameters. Highly responsive and correlated metabolites were identified across the graft collection including malate, citrate, and aspartate, and their variance was partly related to rootstock origin. A group of six metabolites that consistently characterized exceptional graft response was observed, consisting of sorbose, galactose, sucrose, fructose, myo-inositol, and proline. The correlation analysis and predictive modelling, integrating phenotype- and leaf metabolite data, suggest a potential predictive relation between a set of leaf metabolites and yield-related traits.

Genomic structural variation in tomato and its role in plant immunity

It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives.

Haplotype analyses reveal novel insights into tomato history and domestication driven by long-distance migrations and latitudinal adaptations

A novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian societies domesticated species of interest by introducing complex genetic modifications. For tomatoes, two species, one of which had two botanical varieties, are thought to be involved in its domestication: the fully wild Solanum pimpinellifolium (SP), the wild and semi-domesticated Solanum lycopersicum var. cerasiforme (SLC) and the cultivated S. l. var. lycopersicum (SLL). The Procrustes approach showed that SP evolved into SLC during a gradual migration from the Peruvian deserts to the Mexican rainforests and that Peruvian and Ecuadorian SLC populations were the result of more recent hybridizations. Our model was supported by independent evidence, including ecological data from the accession collection site and morphological data. Furthermore, we showed that photosynthesis-, and flowering time-related genes were selected during the latitudinal migrations.

Gamma rays induced genetic variability in tomato (Solanum lycopersicum L.) germplasm

The present study assessed the effectiveness of gamma radiation in inducing favorable genetic variability in tomato (Solanum lycopersicum L.). An experiment was conducted in a randomized complete block design to produce M₁ generation. Significant differences were observed among the genotypes as well as between the treatments at individual plant level based on observed traits (seed germination percentage, seedling survival, plant height, number of flower clusters plant⁻¹, number of flowers and fruits plant⁻¹). All observed characters in the mutagenized population were adversely affected with increasing radiation dose. Results identified 450 Gy as the most damaging radiation dose followed by 300 Gy and 150 Gy. Moreover, 300 Gy treatment was identified as lethal dose (LD₅₀) as it caused a 50% germination inhibition in almost all the evaluated genotypes. The 150 Gy treatment showed the least damaging impact and induced maximum genetic variability in almost all the genotypes under study. Character association studies were also conducted which could be utilized in the selection of desirable mutants. Correlation studies revealed an altered association among the observed parameters from positive to negative direction in 300 Gy and 450 Gy treatments as compared to control. These deviations in correlation coefficients proved that mutagenesis can break the linkage among specific loci. Furthermore, path coefficient analysis identified the growth attributes with an effective direct and indirect contribution in yield.