title: Genomic variation in tomato, from wild ancestors to contemporary breeding accessions.
abstract: BACKGROUND
  Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection.
  
  
  RESULTS
  Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and "cherry tomato" are not synonymous terms. The morphologically-based term "cherry tomato" included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups.
  
  
  CONCLUSIONS
  This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.
authors.affiliation: Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain. jblanca@upv.es.
authors.forename: José
authors.initials: J
authors.lastname: Blanca
authors.affiliation: Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain. jamonpa@upv.es.
authors.forename: Javier
authors.initials: J
authors.lastname: Montero-Pau
authors.affiliation: INRA, UR 1052 Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 67 Allée des Chênes CS60094, 84143, Montfavet Cedex, France. christopher.sauvage@avignon.inra.fr.
authors.forename: Christopher
authors.initials: C
authors.lastname: Sauvage
authors.affiliation: INRA, UR 1052 Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 67 Allée des Chênes CS60094, 84143, Montfavet Cedex, France. Guillaume.Bauchet@avignon.inra.fr.|Syngenta seeds, 12 chemin de l'hobit, 31790, Saint-Sauveur, France. Guillaume.Bauchet@avignon.inra.fr.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bauchet
authors.affiliation: Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH, 44691, USA. illaberenguer.1@osu.edu.
authors.forename: Eudald
authors.initials: E
authors.lastname: Illa
authors.affiliation: Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain. mdiezni@btc.upv.es.
authors.forename: María José
authors.initials: MJ
authors.lastname: Díez
authors.affiliation: Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH, 44691, USA. francis.77@osu.edu.
authors.forename: David
authors.initials: D
authors.lastname: Francis
authors.affiliation: INRA, UR 1052 Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 67 Allée des Chênes CS60094, 84143, Montfavet Cedex, France. mcausse@avignon.inra.fr.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Causse
authors.affiliation: Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH, 44691, USA. vanderknaap.1@osu.edu.
authors.forename: Esther
authors.initials: E
authors.lastname: van der Knaap
authors.affiliation: Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain. jcanizares@upv.es.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Cañizares
mesh_terms: D001947:Breeding; D019143:Evolution, Molecular; D005638:Fruit / Q000235:genetics; D005787:Gene Frequency; D018745:Genome, Plant; D023281:Genomics; D006579:Heterozygote; D018551:Solanum lycopersicum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide