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

Pepper(Capsicum spp.)is one of the most important vegetable crops;however,pepper genomic studies lag behind those of other important Solanaceae.Here we present the results of a high-throughput genotyping-by-sequencing(GBS)study of a collection of 190 Capsicum spp.accessions,including 183 of five cultivated species(C.annuum,C.chinense,C.frutescens,C.baccatum,and C.pubescens)and seven of the wild form C.annuum var.glabriusculum.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.C.annuum,C.baccatum,and C.chinense were successfully separated by all methods.Our population was divided into seven clusters by DAPC,where C.frutescens accessions were clustered together with C.chinense.C.annuum var.glabriusculum 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 C.annuum 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.

Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy S.pimpinellifolium and S.lycopersicum var.cerasiforme accessions used for the first interspecific tomato MAGIC population

The wild Solanum pimpinellifolium(SP)and the weedy S.lycopersicum var.cerasiforme(SLC)are largely unexploited genetic reservoirs easily accessible to breeders,as they are fully cross-compatible with cultivated tomato(S.lycopersicum var.lycopersicum).We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions,selected to maximize the range of variation of both taxa.These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross(MAGIC)population.The morphoagronomic characterization was carried out with 39 descriptors to assess plant,inflorescence,fruit and agronomic traits,revealing the broad range of diversity captured.Part of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments,while in the case of SLC to both human activity and adaptation to the environment.Whole-genome resequencing of the eight accessions revealed over 12 million variants,ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP,being 46.3%of them(4,897,803)private variants.The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC.This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa.The functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and breeding.The comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes.