Nuclear intron-targeting markers in genetic diversity analysis of black nightshade (Solanum sect. Solanum, Solanaceae) accessions

Different molecular markers are routinely used in studies of potato (Solanum tuberosum) and the genus Solanum in general. Genome sequence databases provide potential to design new markers for various applications. Here we present the application of a recently developed core set of nuclear intron-targeting (indel) markers. These markers are based on the fact that in the plant genome introns are more variable than exons; therefore primers flanking exons can reveal polymorphisms related to introns. We detected such variation among accessions of the
eight different species of black nightshades (Solanum sect. Solanum). Members of this group are important sources of food, mostly in Africa, while others are poisonous weeds with near global distribution. The ested 29 primers were designed previously for potato based on Solanaceae EST and other genomic databases and targeted 16 different genes. Our results showed that Solanum intron-targeting markers are not very polymorphic but identified considerable structure among accessions indicating fairly high interspecies differentiation. Further analyses showed that inbreeding is unlikely to be the major driving force in determining the genetic structure of the analyzed species. All phylogenetic analyses resolved the species included in our study as distinct clades with high support values, but provided weak information about their internal relationships. In summary, indel markers would be
useful for the assignment of new Solanum germplasm to taxonomic groups or to identify certain taxa. They could also be used to address important question about genetic diversity and should yield results comparable to other markers covering the whole genome.