MSc.

Chilli (Capsicum spp.) is considered as one of the most important commercial spice crops and is
a widely used universal spice, named as the wonder spice. It is raised over an area of 18 lakh ha.
in the world, with a production of 29 lakh t. India is not only the largest producer but also the
largest consumer of chilli in the world.

The study entitled “DNA fingerprinting of selected chilli (Capsicum spp.) varieties” was carried
out at the Centre for Plant Biotechnology and Molecular Biology, College of Horticulture during
the period 2012-2013. The objectives of the study were to characterize the released chilli
varieties of KAU using different molecular markers- RAPD, ISSR and SSR and to develop DNA
fingerprint with which the variety could be identified and its fidelity detected.

Six chilli varieties, namely Ujwala, Anugraha, Jwalamukhi, Jwalasakhi, Vellayani Athulya and
Vellayani Samrudhi collected from CoH, Vellanikkara and CoA, Vellayani and maintained at
CPBMB, CoH were used for the study. Morphological parameters of six chilli varieties were
taken such as stem colour, branching habit, leaf size, leaf colour, fruit colour, fruit shape and
fruit surface. DNA extraction was done by CTAB (Rogers and Bendich, 1994) method. The
RNA contamination was completely removed through RNase treatment. Good quality DNA with
UV absorbance ratio (A
260
/A
) 1.80 - 1.91 was used for further analysis.

The PCR conditions were optimized for RAPD, ISSR and SSR assays. Thirty RAPD, 30 ISSR
and 30 SSR primers were screened with bulked DNA of Ujwala, Anugraha and Jwalamukhi
variety for amplification and those which gave reliable distinct banding patterns were selected
for further amplification and fingerprinting. The PCR products obtained from RAPD, ISSR and
SSR analyses were separated on two per cent agarose gel and the amplification patterns were
recorded. Genomic DNA from each variety was amplified with ten selected primers of RAPD,
ISSR and SSR primer pairs. The amplification patterns were scored and depicted to develop
DNA fingerprint for each variety. The Resolving power (Rp) worked out for the different primers ranged between 8.33 (S 12) to
12.9 (OPAH 06) for RAPD primers and 8.66 (SPS 03) to 14.33 (ISSR 07) for ISSR primers,
indicating the capacity of the primers selected to distinguish the varieties. The Polymorphic
Information Content (PIC) varied from 0.80 (S 12) to 0.86 (OPAH 06) for RAPD primers and it
was 0.82 (SPS 03) to 0.88 (UBC 840) for ISSR primers.

Distinct bands were used to develop DNA fingerprint of chilli varieties (Ujwala, Anugraha,
Jwalamukhi, Jwalasakhi, Vellayani Athulya and Vellayani Samrudhi) through RAPD, ISSR and
SSR analyses. Sharing of amplicons developed for each primer with other varieties was also
analyzed and demarcated with different colour codes in the fingerprints developed. Most of the
amplicons were found shared among the varieties. However, the pattern of sharing was different
and good enough to separate out the varieties. Combined DNA fingerprint for each variety with
RAPD, ISSR and SSR data was also developed.

The amplification patterns observed in RAPD, ISSR and SSR analyses were scored and analyzed
for quantifying the variability among the varieties. The computer software NTSYS-Pc was used
for cluster analysis (Rohlf, 2005). Maximum variability observed was 41 per cent for the variety
Vellayani Samrudhi. The varieties Ujwala and Anugraha indicated 91 per cent similarity. The
fingerprint developed was sufficient to provide varietal identity and the analysis could reveal
variability/ relatedness among the six varieties.