Growth and antioxidant responses to water stress in eggplant MAGIC population parents, F1 hybrids and a subset of recombinant inbred lines.

BACKGROUND: The generation of new eggplant (Solanum melongena L.) cultivars with drought tolerance is a main challenge in the current context of climate change. In this study, the eight parents (seven of S. melongena and one of the wild relative S. incanum L.) of the first eggplant MAGIC (Multiparent Advanced Generation Intercrossing) population, together with four F1 hybrids amongst them, five S5 MAGIC recombinant inbred lines selected for their genetic diversity, and one commercial hybrid were evaluated in young plant stage under water stress conditions (30% field capacity; FC) and control conditions (100% FC). After a 21-day treatment period, growth and biomass traits, photosynthetic pigments, oxidative stress markers, antioxidant compounds, and proline content were evaluated. RESULTS: Significant effects (p < 0.05) were observed for genotype, water treatments and their interaction in most of the traits analyzed. The eight MAGIC population parental genotypes displayed a wide variation in their responses to water stress, with some of them exhibiting enhanced root development and reduced foliar biomass. The commercial hybrid had greater aerial growth compared to root growth. The four F1 hybrids among MAGIC parents differed in their performance, with some having significant positive or negative heterosis in several traits. The subset of five MAGIC lines displayed a wide diversity in their response to water stress. CONCLUSION: The results show that a large diversity for tolerance to drought is available among the eggplant MAGIC materials, which can contribute to developing drought-tolerant eggplant cultivars.

Nitrogen use efficiency, growth and physiological parameters in different tomato genotypes under high and low N fertilisation conditions.

Identification of novel genotypes with enhanced nitrogen use efficiency (NUE) is a key challenge for a sustainable tomato production. In this respect, the performance of a panel of thirty tomato accessions were evaluated under high (HN; 5 mM N) and low (LN; 0.5 mM N) nitrogen irrigation solutions. For each treatment, when 50% of plants reached the first flower bud stage, plant growth and biomass traits, chlorophyll, flavonol and anthocyanin indexes, nitrogen balance index (NBI), C:N ratio in leaves, stems, and roots, and NUE were evaluated. Significant (p < 0.05) effects were observed for accession, N treatment, and their interaction across all the traits. Under LN, plants showed a delayed development (40 days for HN vs. 65 days for LN) and reduced growth and biomass. On average, LN condition led to 41.8% decrease in nitrogen uptake efficiency (NUpE) but also 189.0% increase in NUtE, resulting in 62.2% overall increase in NUE. A broad range of variation among accessions was observed under both HN and LN conditions. Under LN conditions, chlorophyll index and NBI decreased, while flavonol and anthocyanin indexes increased. Leaf C:N ratio was positively correlated with nitrogen utilisation efficiency (NUtE) in both N treatments. Multi-trait analyses identified top-performing accessions under each condition, allowing to identify one accession among top performers under both conditions. Correlation analysis revealed that high root biomass and leaf C:N ratio are useful markers for selecting high NUE accessions. These findings offer valuable insights for improving tomato NUE under varying nitrogen fertilization conditions and for breeding high-NUE cultivars.

Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes.

Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena, similar to what was described for other fruit-bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving 'local' phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P-SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.

Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato.

European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic, and geographical diversity present in European traditional tomatoes, to investigate the basis of their phenotypic variation, gene×environment interactions, and stability for 33 agro-morphological traits. Comparison of the traditional varieties with a modern reference panel revealed that some traditional varieties displayed excellent agronomic performance and high trait stability, as good as or better than that of their modern counterparts. We conducted genome-wide association and genome-wide environment interaction studies and detected 141 quantitative trait loci (QTLs). Out of those, 47 QTLs were associated with the phenotype mean (meanQTLs), 41 with stability (stbQTLs), and 53 QTL-by-environment interactions (QTIs). Most QTLs displayed additive gene actions, with the exception of stbQTLs, which were mostly recessive and overdominant QTLs. Both common and specific loci controlled the phenotype mean and stability variation in traditional tomato; however, a larger proportion of specific QTLs was observed, indicating that the stability gene regulatory model is the predominant one. Developmental genes tended to map close to meanQTLs, while genes involved in stress response, hormone metabolism, and signalling were found within regions affecting stability. A total of 137 marker-trait associations for phenotypic means and stability were novel, and therefore our study enhances the understanding of the genetic basis of valuable agronomic traits and opens up a new avenue for an exploitation of the allelic diversity available within European traditional tomato germplasm.

Evaluation of three sets of advanced backcrosses of eggplant with wild relatives from different gene pools under low N fertilization conditions.

The development of new cultivars with improved nitrogen use efficiency (NUE) is key for implementing sustainable agriculture practices. Crop wild relatives (CWRs) provide valuable genetic resources for breeding programs aimed at achieving this goal. In this study, three eggplant (Solanum melongena) accessions together with their advanced backcrosses (ABs; BC3 to BC5 generations) were evaluated for 22 morpho-agronomic, physiological, and NUE traits under low nitrogen (LN) fertilization conditions. The ABs were developed with introgressions from the wild relatives Solanum insanum, Solanum dasyphyllum, and Solanum elaeagnifolium. The AB population comprised a total of 25, 59, and 59 genotypes, respectively, with overall donor wild relative genome coverage percentages of 58.8%, 46.3%, and 99.2%. The three S. melongena recurrent parents were also evaluated under control (normal) N fertilization. Reduction of N fertilization in the parents resulted in decreased chlorophyll content-related traits, aerial biomass, stem diameter, and yield and increased NUE, nitrogen uptake efficiency (NUpE), and nitrogen utilization efficiency (NUtE). However, the decrease in yield was moderate, ranging between 62.6% and 72.6%. A high phenotypic variation was observed within each of the three sets of ABs under LN conditions, with some individuals displaying improved transgressive characteristics over the recurrent parents. Using the single primer enrichment technology 5 k probes platform for high-throughput genotyping, we observed a variable but high degree of recurrent parent genome recovery in the ABs attributable to the lines recombination, allowing the successful identification of 16 quantitative trait loci (QTL). Different allelic effects were observed for the introgressed QTL alleles. Several candidate genes were identified in the QTL regions associated with plant growth, yield, fruit size, and NUE-related parameters. Our results show that eggplant materials with introgressions from CWRs can result in a dramatic impact in eggplant breeding for a more sustainable agriculture.

Conventional and new genetic resources for an eggplant breeding revolution.

Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.

Comparative Analysis of Phenotypic and Molecular Data on Response to Main Pear Diseases and Pest Attack in a Germplasm Collection.

The pear is an important fruit tree in temperate areas, but due to its sensitivity, fruit yield and quality are often affected by disease and pest attacks. Pear genotypes from a germplasm collection comprising 13 Pyrus species, 17 Romanian varieties, and 50 non-Romanian varieties from a worldwide assortment were investigated in this study. Throughout four years, response to attack of the principal pathogens and pests was investigated phenotypically under natural conditions of infection and infestation. SSR markers were used to analyze the genetic diversity of the genotypes. A standardized method for the evaluation of responses to biotic stressors was proposed, which highlighted significant differences between genotypes. The species and varieties with the lowest degrees of attack (DA%), calculated based on the frequency and intensity of attack, were identified for pear scab (Venturia pyrina), septoria (Septoria pyricola), fire blight (Erwinia amylovora), and psyllids (Psylla sp.). These accessions could provide valuable sources of genes of interest to develop resistant varieties in new pear breeding programs. By combining phenotypic and molecular analyses, significant information was obtained that can be exploited to generate high variability for selection through artificial hybridization by harnessing accessions with complementary molecular fingerprints and high genetic distances.

Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits.

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.

Transgressive Biochemical Response to Water Stress in Interspecific Eggplant Hybrids.

In a climate change scenario, crop tolerance to drought must be urgently improved, as it represents an increasingly critical stress reducing agricultural yields worldwide. Although most crops are relatively sensitive to water stress, many of their wild relatives are more tolerant and may be used to improve drought tolerance in our crops. In this study, the response to drought of eggplant (Solanum melongena), its close wild relatives S. insanum and S. incanum and their interspecific hybrids with S. melongena was assessed. The plants were subjected to two treatments for 18 days: control, with irrigation every four days, and drought, with complete interruption of irrigation. Morphological and biomass traits were measured, and physiological and biochemical responses were analysed using stress biomarkers such as proline, flavonoids, and total phenolic compounds. Oxidative stress was quantified by measuring malondialdehyde (MDA) content. As a result of the drought treatment, plant development and tissue water content were seriously affected. Generally, water deficit also caused significant increases in MDA, proline, flavonoids, and total phenolics compounds. Our results comparing parental accessions reveal a better response to drought in one of the S. insanum accessions. The hybrid between S. melongena and S. incanum displayed a better response than the other hybrids and even its parents. The results obtained here might be helpful for future eggplant breeding programmes aimed at improving drought tolerance.

Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette.

Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes for this trait. A genome-wide association study (GWAS) performed with 420 MAGIC individuals revealed a major association on chromosome 8 close to a gene similar to APRR2. Two variants in SmAPRR2, predicted as having a high impact effect, were associated with the absence of fruit chlorophyll pigmentation in the MAGIC population, and a large deletion of 5.27 kb was found in two reference genomes of accessions without chlorophyll in the fruit peel. The validation of the candidate gene SmAPRR2 was performed by its sequencing in a set of MAGIC individuals and through its de novo assembly in 277 accessions from the G2P-SOL eggplant core collection. Two additional mutations in SmAPRR2 associated with the lack of chlorophyll were identified in the core collection set. The phylogenetic analysis of APRR2 reveals orthology within Solanaceae and suggests that specialization of APRR2-like genes occurred independently in Cucurbitaceae and Solanaceae. A strong geographical differentiation was observed in the frequency of predominant mutations in SmAPRR2, resulting in a lack of fruit chlorophyll pigmentation and suggesting that this phenotype may have arisen and been selected independently several times. This study represents the first identification of a major gene for fruit chlorophyll pigmentation in the eggplant fruit.

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.

Genotypic and Environmental Effects on Morpho-Physiological and Agronomic Performances of a Tomato Diversity Panel in Relation to Nitrogen and Water Stress Under Organic Farming.

The agricultural scenario of the upcoming decades will face major challenges for the increased and sustainable agricultural production and the optimization of the efficiency of water and fertilizer inputs. Considering the current and foreseen water scarcity in several marginal and arid areas and the need for a more sustainable farming production, the selection and development of cultivars suitable to grow under low-input conditions is an urgent need. In this study, we assayed 42 tomato genotypes for thirty-two morpho-physiological and agronomic traits related to plant, fruit, and root characteristics under standard (control) and no-nitrogen fertilization or water deficit (30% of the amount given to non-stressed trials) treatments in two sites (environments), which corresponded to organic farms located in Italy and Spain. A broad range of variation was found for all traits, with significant differences between the applied treatments and the cultivation sites. Dissection of genotypic (G), environmental (E), and treatment (T) factors revealed that the three main factors were highly significant for many traits, although G was the main source of variation in most cases. G × E interactions were also important, while G × T and E × T were less relevant. Only fruit weight and blossom end rot were highly significant for the triple interaction (G × E × T). Reduction of water supply significantly increased the soluble solid content in both locations, whereas both nitrogen and water stress led to a general decrease in fruit weight and total yield. Despite so, several accessions exhibited better performances than the control when cultivated under stress. Among the accessions evaluated, hybrids were promising in terms of yield performance, while overall landraces and heirlooms exhibited a better quality. This suggests the possibility of exploiting both the variation within ancient varieties and the heterosis for yield of hybrids to select and breed new varieties with better adaptation to organic farming conditions, both under optimal and suboptimal conditions. The results shed light on the strategies to develop novel varieties for organic farming, giving hints into the management of inputs to adopt for a more sustainable tomato cultivation.

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.

Biological Traits and Genetic Relationships Amongst Cultivars of Three Species of Tagetes (Asteraceae).

Marigolds (Tagetes spp.) are multifunctional flowering plants belonging to the Asteraceae family, well-known and widespread for their ornamental value and many other uses. In this study, morphological differences and genetic relationships among 21 cultivars of three species of marigold (Tagetes patula, T. erecta and T. tenuifolia) were analysed. Results have revealed obvious differences among genotypes, starting from the morphological characteristics of the seeds and their capacity to germinate to adult plant morphological characteristics, both between cultivars and species. The genotypic differences were manifested in considerable variation in the development of phenological stages and the main morphological traits of plants and flowers. PCA and hierarchical clustering analyses of morphological traits revealed a homogeneous grouping of cultivars within each species, except for Orion, belonging to T. patula, which was closer to T. erecta cultivars. A subset of 13 cultivars from the three species was subjected to SSR analysis, revealing considerable genetic diversity and good separation between T. patula on the one side and T. erecta and T. tenuifolia on the other. The observed heterozygosity was much lower than the expected heterozygosity, revealing a high degree of fixation. The results reveal that the three species evaluated have considerable morphological and genetic diversity, which has important implications for assessing genetic diversity, conserving germplasm and selecting parents for new breeding works in marigolds.

Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant.

Multi-parent advanced generation inter-cross (MAGIC) populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3 Magic EGGplant InCanum, S3MEGGIC; 8-way), constituted by the 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanin presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-insensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence single-nucleotide polymorphisms (SNPs) confirmed a low residual heterozygosity (6.87%), a lack of genetic structure in the S3MEGGIC population, and no differentiation among subpopulations carrying a cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of the founder genomes, suggesting a cryptic selection in favour or against specific parental genomes. Genome-wide association study (GWAS) analysis for PA, FA, and PUC detected strong associations with two myeloblastosis (MYB) genes similar to MYB113 involved in the anthocyanin biosynthesis pathway, and with a COP1 gene which encodes for a photo-regulatory protein and may be responsible for the PUC trait. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1 compared with the tomato genome. Parental genotypes for the three genes were in agreement with the identification of the candidate genes performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.

Grafting vigour is associated with DNA de-methylation in eggplant.

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids.

Physico-Chemical, Nutritional, and Sensory Evaluation of Two New Commercial Tomato Hybrids and Their Parental Lines.

Tomato (Solanum lycopersicum) is the globally most consumed vegetable. The objective of this research was to analyze physico-chemical, nutritional and sensorial components (taste and flavor) in two new commercial hybrids (AS 300 F1 and AS 400 F1) and their four F7 parental lines. Two widely grown F1 hybrids (Precos F1 and Addalyn F1) were used as controls. The results obtained for carbohydrates (HPLC-RID) indicated that the highest values (27.82 mg/g) were recorded in the paternal line AS 10 of the new hybrid AS 400 F1. The highest values of total organic acids (HPLC-VWD) were recorded in Addalyn F1 (5.06 m/g), while the highest value of phenolic compounds (HPLC-DAD-ESI⁺) were identified in the maternal line AS 09 of the hybrid AS 400 F1 (96.3 µg/g). Intrinsic sensory values were analyzed by male and female tasters of different ages using a hedonic scale. The tasters' perception revealed obvious taste differences between tomato genotypes. The study allowed determining genetic parameters of interest (heterosis and heterobeltosis) for the new hybrids, as well as a detailed characterization of the chemical composition and organoleptic quality of the parental breeding lines and their hybrids, which is useful in tomato breeding.

Genome wide association mapping for agronomic, fruit quality, and root architectural traits in tomato under organic farming conditions.

BACKGROUND: Opportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Large panels of tomato varieties represent a valuable resource of traits of interest under sustainable cultivation systems and for genome-wide association studies (GWAS). For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we used a heterogeneous set of 244 traditional and improved tomato accessions grown under organic field trials. Here we report comprehensive phenotyping and GWAS using over 37,300 SNPs obtained through double digest restriction-site associated DNA (dd-RADseq). RESULTS: A wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most traits. A variable level of heritability was observed with values up to 69% for morphological traits while, among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has been a minor objective for breeding activities. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families. Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits. CONCLUSIONS: Results of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.