The progress in plant breeding rests on the availability of genetic diversity.  Assessment of genetic variability has impact both in terms of crop improvement as well as for the efficient conservation and management of genetic resources.  Information on genetic diversity can be obtained through DNA fingerprinting approaches which are capable of analyzing large number of loci with extensive variability.

The present study was initiated to assess diversity among 47 chilli germplasm accessions belonging to the species C. annuum collected from different sources along with four released varieties.  Twenty five selected SSR primers were used.  All the primers were initially evaluated for their annealing temperature using a gradient PCR technique.  A total of 59 alleles were detected with an average of 2.5 alleles per locus.  The maximum number of alleles detected was five in two primers and one in 10 primers.  Among the 25 primers screened, 11 primers exhibited a large number of null-alleles and hence only 14 informative primer pairs were selected for cluster analysis.

At these 14 loci, a total of 31 alleles were scored including 8 monomorphic loci.  The pair-wise similarity based on dice-coefficient for all the 47 accessions ranged from 0.73 to 1.  The cophenetic correlation co-efficient (r) computed between the observed distances and the dendrogram was 0.83 which indicates a good fit between observed distances and the dendrogram.  The clustering revealed absence of significant geographical associations.

Further, AFLP diversity of 47 chilli accessions was studied using seven primer combinations, which yielded a total of 5458 scorable bands at 237 loci of which 12% were monomorphic.

Average number of bands / primer combinations ranged from 7.57 (ES2/MS4) to 45.2 (ES1/MS2).  Pair-wise similarity coefficient among the 47 accessions ranged from 0.68 to 0.85.  The cophenetic correlation co-efficient (r) computed between the observed distances and the dendrogram was 0.69.  The cophenetic correlation co-efficient (r) between the observed and the PCoA plot was 0.54.  Geographic associations were better indicated by the AFLPs rather than the SSRs.  The high polymorphism between the accessions obtained with AFLPs may be a reflection of the highly divergent group of paprika chillies included in this study.   The use of a larger number of SSRs with greater genome coverage could help to reveal genetic diversity more accurately.