Page 13 - Molecular Plant Breeding

Molecular Plant Breeding 2012, Vol.3, No.2, 11 -25
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20
bility) has also been studied in a number of genera
including Zostera, Cucumis, Glycine , Trifolium, Brassica,
Vitis, Cajanus and Arachis, where it ranged from 5%
to 100% (Thomas and Scott, 1993; Katzir et al., 1996;
Szewc-McFadden et al., 1996; Peakall et al., 1998;
Rossetto et al., 2001; Zhang et al., 2007; Odeny et al.,
2007; Gautami et al., 2009). Only 9.30% SSRs of C.
olitorius showed null alleles in C. capsularis genotypes
during the present study (Supplementary Table 1).
This may be due to possible mutations at the 3'-end of
the primer binding site in C. capsularis or due to
complete lack of the corresponding SSRs in C.
capsularis or both.
It may be recalled that 5 SSRs detected two loci each
in either one or both the species suggesting that rarely
SSRs may be duplicated in the two species of jute. In
the past also, specific SSRs were reported to detect
more than one locus in different plant systems (Roder
et al., 1998; Stephenson et al., 1998; Prasad et al.,
2000; Belaj et al., 2003). The average number of
alleles per locus (3.46) observed during the present
study is higher than those reported in our earlier study
involving 45 SSRs with 81 genotypes (Mir et al.,
2008b). This may be attributed to the use of a larger
and diverse set of jute genotypes and large number of
SSRs used during the present study. However, in some
earlier studied self-pollinated crops namely rice,
sesame, wheat (Ming et al., 2010; Cho et al., 2011;
Mir et al., 2011) and in a cross-pollinated crop citrus
(Barkley et al., 2006), the average number of alleles
per locus (6.15 to 11.5 alleles per locus) and PIC per
locus (0.420 to 0.716) was relatively higher than those
reported in each of the two jute species during the
present study. These attributes suggested narrow
genetic variability in the two cultivated species of
jute. It may be recalled that 24 SSR loci showed
polymorphism unique to C. capsularis and 52 SSR
loci showed polymorphism unique to C. olitorius
(Table 2). These SSRs may certainly prove useful in
easy discrimination of the genotypes belonging to the
two cultivated species of jute. A substantial number of
unique and some genotype specific alleles (rare alleles)
also suggested that the two species are quite diverse.
2.2 Genetic diversity among the two species
Using UNJ dendrogram and the PCA analyses (Figure
2; Figure 3), the two cultivated species of jute were
shown to be quite diverse forming separate clusters.
Similar results were reported in earlier studies in jute
using chloroplast SSRs, genomic SSRs, ISSRs, AFLP
and RAPD (Basu et al., 2004; Mir et al., 2008b;
Hossain et al., 2002; Roy et al., 2006). The divergence
between the two cultivated species was also indicated
by the results of AMOVA (63% variation between the
two species). This is not surprising in view of the
allopatric distribution and cross incompatibility
between the two species. The grouping of some
genotypes of C. capsularis together with the genotypes
of C. olitorius was observed in the UNJ dendrogram
as well as in PCA plots. These genotypes perhaps
share a large number of alleles (shared alleles, see
Table 1) between the two species leading to their
grouping in a single cluster.
We also examined the clustering pattern (UNJ dendro-
ms and PCA) and structure of the genotypes of the
two jute species separately (Figure 2; Figure 3 and
Figure 5). Most of the genotypes of the indigenous
and exotic collections of the two species were clearly
delineated into separate clusters, although a few
indigenous and exotic genotypes of each of the two
species were also grouped together in separate clusters
(Figure 2b, 2c). However, population structure revealed
only two sub-populations for each of the two jute
species (Table 9; Figure 5), each sub-population having
both indigenous and exotic genotypes of jute and thus,
partially resembling the results of the dendrograms
and PCA plots. The above results suggest the exchange
of germplasm between different countries and also the
use of exotic germplasm in hybridization programs
aimed at jute improvement in India (Kar et al., 2010).
2.3 Genetic differentiation among indigenous and
exotic collections of genotypes and sub-populations
The values of pair-wise GD and Fst between the
indigenous and exotic collections (see Table 8) as well
as the two sub-populations of the two species (discussed
in Results, not shown in Table 8) suggested poor
differentiation between the genotypes of indigenous
and exotic collections. This was also supported by
AMOVA, where very low level of variation (~10%)
observed between indigenous and exotic collections
compared to nine fold (~90%) higher variation within