Inter- and intraspecific differentiation of Capsicum annuum and Capsicum pubescens using ISSR and SSR markers

- ISSR and SSR markers were useful in distinguishing the two tested Capsicum species.
- ISSR and SSR markers efficiently allowed differentiation C. annuum from C. pubescens.
- SSR markers originally designed for C. annuum amplified in C. pubescens.
- SSR markers show cross-transferability due to high genetic homology between both species.

Mexico is the second largest producer of Capsicum sp. fruit, the main consumer worldwide of Capsicum, and the country with the highest genetic diversity of Capsicum. Polymorphism was evaluated in two Serrano and two Jalapeño cultivars of Capsicum annuum and one cultivar of Capsicum pubescens. Cultivar differentiation was performed using molecular characterization with ISSR and SSR markers. Using eight ISSR anchored primers, a total of 38 bands were obtained. Band number varied from 15 to 23 by primer and fragment size from 150 to 6000 bp. Two markers provided polymorphic data. Mean values were 0.77 for PIC, 0.74 for MI and 16.08 for Rp. The number of alleles per marker identified using SSR markers in both species ranged from 1 to 10. Average PIC values for the SSR were 0.5. Both techniques were useful in distinguishing the two tested Capsicum species. Based on PCA and cluster analysis, both techniques efficiently allowed differentiation of the varieties of C. annuum from the C. pubescens, and among varieties of C. annuum, except one variety of Serrano that was grouped with the Jalapeno ones. SSRs used in this study, originally designed for C. annuum, resulted in amplification in C. pubescens, which demonstrated their usefulness for this species as well because these markers include genes that preserve the same coding regions.