Diversity patterns in the Espelette pepper landrace

Crop landraces are valuable reservoirs of genetic variation shaped by local environmental and long-term farmer management. Through decades, landraces have supported conservation, management and improvement of crops. The Espelette pepper (Capsicum annuum L.) is a traditional pepper landrace cultivated in the Basque region of France under a Protected Designation of Origin (PDO) representing a unique geographically and traditionally defined genetic resource. To date, the diversity of Espelette pepper has not been systematically assessed. Our study thus, aims to characterize the genetic, phenotypic and metabolomic diversity of the Espelette population under farmer managed conditions. Data from more than 700 plants were taken across 23 farmers within the PDO region. Genetic diversity and population structure were evaluated using 15000 genome-wide SNP markers genotyped through single primer enrichment technology (SPET) while phenotypic variation was assessed through field-based measurements of various plant developmental, disease and fruit traits as well as metabolomic profiling. The results provide insights into the extent and distribution of variation within the landrace population. As a part of ANR COMBINE project, this work contributes to the integration of genomic and phenotypic information for effective management and conservation of the Espelette pepper.