Unlocking the European traditional tomato genetic resources

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. To unveil the molecular basis of Southern European tomato phenotypic diversity, we carried out the most comprehensive phenotypic and genomic variability analysis on traditional European tomato by using 1) a collection of 1,499 traditional European tomatoes (TRADITOM collection) and 2) a multipurpose core collection (TCC), comprising 227 European traditional tomato accessions from the original TRADITOM collection, that captured most of genotypic and phenotypic variation and geographical origin present in traditional tomatoPostprint (published version

American and european tomato history unveiled using haplotype and GBS analyses

Not many historical or archeological records remain from the tomato journey from Solanum pimpinellifolium (SP) to the vintage varieties, however, its domestication, migrations and diversification in Europe can be unveiled using genetic analyses. The study of 628 SP, Solanum lycopersicum var. cerasiforme (SLC), and Solanum lycopersicum var. lycopersicum (SLL) revealed: 1) SP evolved into SLC during a migration from Peru and Ecuador, 2) there is a wild SLC Mesoamerican population, 3) there are no wild SLC populations in Ecuador and Peru, 4) Peruvian and Ecuadorian SLC are an admixture of Mesoamerican SLC and SP, 5) SP introgressions in SLC harbor flowering control and light response genes, 6) at least some Mesoamerican SLL derives from domesticated Peruvian and Ecuadorian SLC. A GBS analysis of 1,254 accessions,Postprint (published version

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 germplasmThis work was supported by European Commission H2020 research and innovation program through TRADITOM grant agreement no. 634561, G2P-SOL, grant agreement no. 677379, and HARNESSTOM grant agreement no. 101000716. Networking activities were funded by COST Actions “EUROCAROTEN CA15136 and ‘RoxyCOST’ CA18210 ‘RoxyCOSTPostprint (published version

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.This work was supported by the European Commission H2020 research and innovation program through TRADITOM grant agreement no. 634561, G2P-SOL, grant agreement no. 677379, and HARNESSTOM grant agreement no. 101000716. MP is grateful to the Spanish Ministerio de Ciencia e Innovación for a postdoctoral grant (IJC2019-039091-I/AEI/10.13039/501100011033).Postprint (published version

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

[EN] The high phenotypic diversity observed among European traditional tomato varieties was created by traditional farmer-driven selection by inadvertently combining a very few polymorphic loci subjected to balancing selection. 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.This work was supported by the European Commission H2020 research and innovation program through TRADITOM grant agreement no. 634561, G2P-SOL, grant agreement no. 677379, and HARNESSTOM grant agreement no. 101000716. MP is grateful to the Spanish Ministerio de Ciencia e Innovacion for a postdoctoral grant (IJC2019-039091-I/AEI/10.13039/501100011033).Blanca Postigo, JM.; Pons Puig, C.; Montero-Pau, J.; Sánchez-Matarredona, D.; Ziarsolo, P.; Fontanet, L.; Fisher, J.... (2022). European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci. Journal of Experimental Botany. 73(11):3431-3445. https://doi.org/10.1093/jxb/erac07234313445731

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

[EN] 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.We thank Universitat Illes Balears, the Greek Gene Bank (GGB-NAGREF), Universita degli Studi Mediterranea Reggio Calabria, the CRB-Leg (INRA-GAFL)", the Genebank of CNR-IBBR (Bari, Italy) and ARCA 2010 for seed sharing. CNR-IBBR also acknowledges the seed donors, the Leibniz Institute of Plant Genetics and Crop Plant Research, Maria Cristina Patane (CNR-IBE, Catania, Italy) and La Semiorto Sementi SRL, as well as Mrs. Roberta Nurcato for technical assistance. IBMCP-UPV acknowledges Maurizio Calduch (ALCALAX) for technical assistance and Mario Fon for English grammar editing. This work was supported by European Commission H2020 research and innovation program through TRADITOM grant agreement No.634561, G2P-SOL, grant agreement No. 677379, and HARNESSTOM grant agreement No. 101000716. Clara Pons and Mariola Plazas are grateful to Spanish Ministerio de Ciencia e Innovacion for postdoctoral grants FJCI-2016-29118 and IJC2019-039091I/AEI/10.13039/501100011033; Joan Casals to a Serra Hunter Fellow at Universitat Politècnica de Catalunya.Pons Puig, C.; Casals, J.; Palombieri, S.; Fontanet, L.; Riccini, A.; Rambla Nebot, JL.; Ruggiero, A.... (2022). Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato. Horticulture Research. 9:1-16. https://doi.org/10.1093/hr/uhac112116

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