Microsatellite (SSR) Markers Application in the Characterization of Genetic Diversity in Capsicum annuum Germplasm

This study focused on the genetic diversity of Capsicum annuum (commonly known as chili or bell pepper) using 40 Simple Sequence Repeat (SSR) markers across 133 genotypes. Out of 40 SSR markers, 29 were polymorphic, indicating considerable genetic variation within the genotypes. The polymorphic information content (PIC) values ranged from 0.098 to 0.992, with an average of 0.708, reflecting a broad spectrum of genetic information. Notably, 22 markers had PIC values greater than 0.5, demonstrating strong discriminatory power. Among SSRs, the marker AVRDC-17 exhibited the highest PIC value at 0.992, followed by AVRDC 174 (0.990), Agi96 (0.967), and HPMS 1-5 (0.961). The expected heterozygosity (He) of the genotypes varied from 0.038 to 0.766, with an average of 0.428. The marker HPMS 1-214 showed the highest expected heritability value of 0.766, a high level of genetic variability in certain genotypes. Cluster analysis grouped the genotypes into seven distinct genetic clusters, reinforcing the presence of considerable genetic differentiation among the genotypes. Genetic similarity coefficients ranged from 0.11 to 0.91, reflecting the diverse genetic relationships within the population. The highest similarity was observed between genotypes 36569 and 36627, with a coefficient of 0.91, indicating a close genetic relationship. These findings confirm the usefulness of SSR markers in assessing genetic diversity, offering valuable information for breeding programs aimed at developing improved Capsicum annuum cultivars with enhanced yield and adaptability.