This paper describes the isolation and characterization of microsatellite loci inCapsicum frutescens varieties cultivated in Borneo, Malaysia. A total of 58 putative microsatellites distributed across 29 sequences were isolated from a genomic library enriched for microsatellites. Ten locus specific polymorphic molecular markers were developed and applied to determine the levels of genetic diversity across the cultivated population. The expected heterozygosity ranged from 0.4316 - 0.6684 (mean 0.5958) and the observed heterozygosity ranged from 0 - 1 (mean 0.6000). There was a deficiency of heterozygotes within the total population which implies that most of the cultivated varieties in the region have been derived as a result of inbreeding. The estimation of the total genetic diversity of a cultivated crop variety within a geographic region can provide an indication of the extent to which traditional cultivators are relying on inbred varieties of seeds for crop production.
Key words: Capsicum frutescens, bird's eye chili, inosine, microsatellites, heterozygosity.
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