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

Jose Blanca, Clara Pons, Javier Montero-Pau, David Sanchez-Matarredona, Peio Ziarsolo, Lilian Fontanet, Josef Fisher, Mariola Plazas, Joan Casals, Jose Luis Rambla, Alessandro Riccini, Samuela Pombarella, Alessandra Ruggiero, Maria Sulli, Stephania Grillo, Angelos Kanellis, Giovanni Giuliano, Richard Finkers, Maria Cammareri, Silvana GrandilloAndrea Mazzucato, Mathilde Causse, Maria Jose Díez, Jaime Prohens, Dani Zamir, Joaquin Cañizares, Antonio Jose Monforte*, Antonio Granell*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)3431-3445
Number of pages15
JournalJournal of Experimental Botany
Volume73
Issue number11
DOIs
StatePublished - 2 Jun 2022

Bibliographical note

Publisher Copyright:
© 2022 The Author(s) 2022.

Keywords

  • Crop evolution
  • Diversification
  • Fruit morphology
  • Genome-wide association study
  • Genotyping by sequencing
  • Selection
  • Single nucleotide polymorphism

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