PhD

Capsicum
is a unique genus coming under the family Solanaceae. This
genus includes nearly 40 species among which five viz. C. annuum, C.chinense, C.
frutescens, C. baccatum and C. pubescens are cultivated. Large number of types,
the transitory nature of these types, introgressive hybridization and environmental
influence make species arrangement in Capsicum a confusing task. Even though
Kerala is rich in the diversity of Capsicum, a comprehensive study of landraces
available has not yet been carried out. In this background, the present project was
carried out with the objective of characterizing the landraces of Capsicum species
in Kerala using morphological markers and validating the key for the identification
of different taxa using molecular and biochemical markers.
Ripened fruit samples of 262 accessions were collected from the different
districts of Kerala during December, 2013 to August, 2014. These accessions were
planted in augmented block design along with released varieties from Kerala
Agricultural University as checks at National Bureau of Plant Genetic Resources,
Regional Station, Thrissur.
Morphological characterization was done by considering both qualitative
and quantitative characters. Numerical Taxonomy and Multivariate Analysis
System (NTSYS) software version 2.10 z was used for construction of phenogram
based on forty four qualitative characters available in the Capsicum descriptor
(IPGRI, 1995). Accessions belonging to three species viz., C. annuum, C.chinense
and C. frutescens formed species specific clusters. C. baccatum accessions
clustered with C. frutescens. C. chinense accessions were clearly separated and
distantly placed from C. annuum accessions revealing genetic dissimilarity
between the above two species.. Out of 42 clusters formed at 70 per cent similarity
level, 39 are mono-specific clusters. Morphological characterization based on

qualitative unit characters aligned 95 per cent of the accessions into species
specific clusters.
Diversity relationship accessed on the basis of 32 quantitative characters
grouped the accessions into 14 clusters. C. annuum accessions formed mono-
specific clusters where as C. chinense and C. frutescens accessions grouped
together in three different clusters revealing that C. frutescens and C. chinense are
inseparably related. C. annuum accessions were found standing as a separated
group. C. baccatum accessions clustered along with C. frutescens - C. chinense
group.
Representative accessions selected from each qualitative cluster along with
eight released varieties were analysed using 17 RAPD primers. Dendrogram
consisted of eleven mono-specific clusters indicating the ability of RAPD markers
to align the genotypes into correct taxa. Clustering of C. annuum accession with C.
frutescens (two clusters) and C. chinense (two clusters) as well as clustering
between C. frutescens and C. chinense (three clusters) accessions points to the
genetic similarity within the annuum complex. C. baccatum accession expressed
more similarity with C. frutescens.
The genetic background of the annuum complex was further scrutinized
with 18 SSR primers among 19 genotypes comprising of eight C. annuum, seven
C. chinense and four of C. frutescens accessions. Out of five clusters formed, two
were mono-specific C. annuum clusters. Other three clusters composed of both C.
frutescens and C. chinense accessions in each clusters. Thus SSR characterization
clearly revealed the close genetic similarity between C. frutescens and C. chinense
species and this group is distantly placed from C. annuum species. Clustering
pattern based on RAPD primers for the above 19 genotypes strongly supported the
result of SSR analysis with formation of two major clusters viz., one composed of
C. annuum type only and the other major cluster comprising both species viz., C.
frutescens and C. chinense. Dendrogram constructed based on RAPD and SSR
banding pattern also substantiated above result by forming mono-specific C.
annuum clusters and clusters comprising accessions from both species viz., C.
frutescens and C. chinese.

Both RAPD and SSR analysis points to the close similarity among the
released varieties. All the released varieties of C. annuum type are grouped in to
the same cluster. Combined analysis based on RAPD and SSR data resulted in the
formation of two major clusters viz., first cluster comprising of only released
varieties and second of landraces.
Compared to separate RAPD or SSR characterization, combined analysis
based on RAPD and SSR data more precisely assigned accessions into
corresponding species specific clusters and formed mono-specific clusters. At 70
per cent similarity level, combined RAPD-SSR analysis expressed 79 per cent
accuracy for allotting accessions to species specific clusters. More number of
molecular markers improve the accuracy of species alignment and molecular
markers serve a complementary role to assist phenetics.
Quantity of ascorbic acid ranges from 81.40 to 327.58 mg per 100g of ripe
chilly. The upper limit of capsaicin and oleoresin were 0.87 and 23.5 per cent,
respectively. Accessions superior in performance to the check varieties for
economic and biochemical characters were identified through the agronomic
characterization. Majority of the yield contributing characters exhibited high GCV
coupled with moderate to high heritability and high genetic gain revealing wide
variability contributed by genetic factors and indicating scope for selection.
DNA fingerprinting profile of released varieties and elite accessions were
developed using SSR primers. Species specific fingerprinting of C. annuum, C.
chinense and C. frutescens species were also made for differentiation of species
with SSR primers.
Validation of taxonomic key carried out integrating characters viz., spot
colour at the throat of corolla, annular constriction at calyx, number of flowers per
axil, corolla colour, position of flower at anthesis, leaf shape, margin of calyx at
fruiting, fruit to pedicel length ratio and level of main stem bifurcation. SSR
primers viz., CAMS-101, CAMS-806 and CAMS-864 as well as RAPD primers
viz., OPB-10,OPG-02, OPG-03, OPB-08 and OPA-03 identified as promising in
identification and differentiation of cultivated species of Capsicum.