Genetic diversity, population structure, and relationships in a collection of pepper ( spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS).

Pepper ( spp.) is one of the most important vegetable crops; however, pepper genomic studies lag behind those of other important . Here we present the results of a high-throughput genotyping-by-sequencing (GBS) study of a collection of 190 spp. accessions, including 183 of five cultivated species (, , , , and ) and seven of the wild form var. . Sequencing generated 6,766,231 high-quality read tags, of which 40.7% were successfully aligned to the reference genome. SNP calling yielded 4083 highly informative segregating SNPs. Genetic diversity and relationships of a subset of 148 accessions, of which a complete passport information was available, was studied using principal components analysis (PCA), discriminant analysis of principal components (DAPC), and phylogeny approaches. , , and were successfully separated by all methods. Our population was divided into seven clusters by DAPC, where accessions were clustered together with . var. accessions were spread into two distinct genetic pools, while European accessions were admixed and closely related. Separation of accessions was mainly associated to differences in fruit characteristics and origin. Phylogeny studies showed a close relation between Spanish and Mexican accessions, supporting the hypothesis that the first arose from a main genetic flow from the latter. Tajima's D statistic values were consistent with positive selection in the clusters, possibly related to domestication or selection towards traits of interest. This work provides comprehensive and relevant information on the origin and relationships of Spanish landraces and for future association mapping studies in pepper.