Genetic diversity in - chilli (Capsicum annuum L.) based on microsatellite markers: An evaluation of Bangladeshi germplasm

Genetic diversity analysis is a pre-requisite to develop improve variety of any crop. Hence, 39 SSR markers were used to analyze the genetic diversity of local chilli cultivars. PCR-amplified microsatellite loci were shown to be polymorphic in all investigated cultivars. The locus, CAMS-647 produced the highest number of alleles (8) ranging in size from 188 to 279 bp. PIC values for 39 primers ranged from 0.099 for the locus Hpms 1-165 to 0.806 for the locus CAMS-679. All of the SSRs examined were informative in characterizing the genotypic variance of the samples while 12 were more informative with higher PIC values (> 0.6). There was a wide range of genetic diversity varied from 0.117 (HpmsE075) to 0.806 (CAMS-647), whereas the highest (1.713) and the lowest (0.205) value of Shannon’s Information Index was registered in the locus CAMS-679 and Hpms 1-165, respectively. There was a higher degree of genetic differentiation (0.927) and a lower amount of gene flow (0.010). Nei’s genetic distance (GD) varied from 0.100 to 0.990. Among 96 cultivars, 55 had distinct status in the dendrogram with higher GD values (> 0.6), while 41 cultivars showed a close relationship and yielded lower GD values.