Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean = 8.6 bands/primer), of which ~92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPGMA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper germplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.

The Eastern Mediterranean Region has a significant potential for capia pepper production in Turkey. In the region, a population named as 'Karaisali pepper' with special characteristics, is grown. The population is well-adapted to the region and grown for processing. Karaisali pepper is usually preferred for red pepper production due to its high dry matter content. Survey studies conducted on Karaisali pepper in 2014 and 2015 demonstrated that the Tobacco etch virus (TEV) was the most common and destructive virus affecting Karaisali pepper. In the present study, three pure lines derived from Karaisali pepper were used to assess their susceptibilities against TEV. The experiment included mechanically inoculated infected plants and healthy pepper plants in the control group. The pepper plants were inoculated with the TEV using mechanical inoculation method during the four-leaf stage. The plants were observed periodically after mechanical inoculation. Each repetition was analyzed based on the total yield, pepper paste yield, fruit size, soluble solid content, fruit color and market value. The result indicated that, in average, TEV reduced Karaisali pepper yield by 77.5% and pepper paste yield by 33.6%. Furthermore, the average fruit length (37%), fruit diameter (21.4%), fruit wall thickness (14.2%), fruit volume (60.2%) and first quality fruit ratio were also decreased. The results confirm the threats of TEV in pepper production.

The most prevalently grown varieties of red peppers in the Eastern Mediterranean region of Turkey are ‘Sena’ and ‘Dila’ in addition to local red pepper populations. Survey studies conducted on Kahramanmaras pepper growing areas in 2014 and 2015 indicated that Tobacco etch virus (TEV) was the most common virus in collected pepper samples. In this study, the effects of TEV on ‘Sena’ and ‘Dila’ were analyzed. The experiment was designed with 5 replicates and randomized plots in fully controlled greenhouses. The experiment consisted of TEV inoculated and control pepper plots. The pepper plants were mechanically inoculated with TEV at the 4–6 leaf stage and periodical observations were made. Virus transmission was confirmed using the double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) method. The total yield, red pepper flake production, average fruit weight, diameter, length and volume, average fruit wall thickness, fruit color and fresh and dry weights of all green parts of harvested red peppers were evaluated. The quoted data on % reduction in yield and different fruit quality criteria are averaged over two years. According to the results of the study, the highest loss of yield was recorded for ‘Sena’ (58.2%) while the highest red pepper flake loss ratio was in ‘Dila’. In terms of fruit quality criteria, the most reductions in fruit weight (40.1%), fruit diameter (30.9%), fruit length (32.8%) and fruit volume (51.8%) were found in ‘Dila’, the highest losses in fruit wall thickness (27.2%) and average fresh and dry weights of green parts (49.9–43.1%) were in the ‘Sena’. There was a significant effect of TEV inoculation. Overall, virus infected plants were had significantly lower yield and reduced quality compared to control plants.