PCR-Based Profiling of Genetic Variability in Domesticated Capsicum spp.: Implications for Biodiversity

Abstract

The original tropical genus Capsicum spp. is an important crop worldwide, particularly the species C. chinense and C. annuum. Like many crops subjected to long-term domestication and breeding, and under the continuous influence of human activity on the environment, the Capsicum genus faces a significant loss of biodiversity and a gradual reduction in the availability of its genetic resources. This study aimed to evaluate the applicability of existing PCR marker techniques for both interspecific and intraspecific analysis, and to examine the extent of genetic similarity or diversity among the genomes of the cultivated Capsicum spp. Five varieties of C. chinense and C. annuum were used in PCRs to detect genetic variability by four DNA-based dominant marker techniques: CDDP, iPBS, PBA and BBAP. The number of loci for all methods was 310 and it varied from 34 (PBA), 62 (BBAP) and 96 (iPBS) to 117 (CDDP), P% for all methods was 79.68% (45.71% PBA, 82.26% BBAP, 84.38% iPBS and 86.32% CDDP). The CDDP primers had the maximum discriminating power at 0.718, whilst the PBA primers displayed the lowest value at 0.379 among the applied approaches. The pair Ohnivec – Jalahot had the highest genetic similarity across all approaches, evaluated at 0.335. The lowest genetic similarity was detected between the pairings H. chocolate and Ohnivec, reported at 0.629. All used DNA-based marker techniques were evaluated as applicable and informative in the genus Capsicum spp., from moderately informative PBA, through highly informative iPBS and BBAP to very highly informative CDDP.