European traditional tomatoes galore: a result of farmers’ selection of a few diversity-rich loci
Résumé
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.
Mots clés
GBS
Genotyping by sequencing
GWAS
genome-wide association study
LD
linkage disequilibrium
LSL
long shelf-life
MAF
minimum allele frequency
PCoA
principal coordinate analyses
QTL
quantitative trait locus
SLL
Solanum lycopersicum L. var. lycopersicum
SLC
Solanum lycopersicum var. cerasiforme
SNP
single nucleotide polymorphism
SP
Solanum pimpinellifolium HM Clause
Portes-lès-Valence
France Crop evolution
diversification
fruit morphology
genotyping by sequencing
selection
