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Article|17 May 2022|OPEN
Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato
Clara Pons1,2 , Joan Casals3 , Samuela Palombier4,14 , Lilian Fontanet5,13 , Alessandro Riccini6 , Jose Luis Rambla2 , Alessandra Ruggiero4 , Maria del Rosario Figás1 , Mariola Plazas1,2 , Athanasios Koukounaras7 , Maurizio E. Picarella6 , Maria Sulli8 , Josef Fisher9 , Peio Ziarsolo1 , Jose Blanca1 , Joaquin Cañizares1 , Maria Cammareri4 , Antonella Vitiello4 , Giorgia Batelli4 , Angelos Kanellis10 , Matthijs Brouwer11 , Richard Finkers11 , Konstantinos Nikoloudis12 , Salvador Soler1 , Giovanni Giuliano8 , Stephania Grillo4 , Silvana Grandillo4 , Dani Zamir9 , Andrea Mazzucato6 and Mathilde Causse5 , Maria José Díez1 , Jaime Prohens1 , Antonio Jose Monforte2 , , Antonio Granell,2 ,
1Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
2Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
3Department of Agri-Food Engineering and Biotechnology/Miquel Agustí Foundation, Universitat Politècnica de Catalunya, Campus Baix Llobregat, Esteve Terrades 8, 08860 Castelldefels, Spain
4Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
5INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allé des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
6Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
7Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Vegetable Crops, Thessaloniki, 54124 Greece
8Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
9Hebrew University of Jerusalem, Robert H Smith Inst Plant Sci & Genet Agr, Rehovot, Israel
10Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
11Wageningen Univ & Res, Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands
12Agroindustrial Cooperative of Tympaki, 70200 Tympaki, Greece
13Current address: HM Clause, Portes-lès-Valence, France
14Current address: Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy
*Corresponding author. E-mail:,

Horticulture Research 9,
Article number: uhac112 (2022)
Views: 144

Received: 11 Jan 2022
Accepted: 27 Apr 2022
Published online: 17 May 2022


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.