one that belongs to C. chinense Jacq.
The low polymorphic level detected by the primers M2
(EcoRI + ACG/MseI + CAG) and M6 (EcoRI + AGG/MseI
+ CTG) (Table 2) may be the result of the parents
involved in the diallel cross transferring a large portion of
their genomes to their offspring (Brown, 2002). The
presence of polymorphism amplification bands indicated
that variations may have existed in the loci of certain
materials (Shi et al., 2009).
According to Kochieva and Ryzhova (2003), the
genome of the capsicum cultivars evaluated was highly
conserved, because genetic distances were small (0.021-
0.072). However, it may be broken by the recombination
of genomes of different types, as shown in our study in
which genetic distances were greater than those listed
earlier.
Another possible answer could be that the germplasm
used as parents belongs to two different species of chili.
Thus, a hybrid performance prediction based on genetic
distances is not easy, as subgroups are formed among
the parents and crosses, influenced by the species to
which they belong, as seen in Figures 1 and 2. This
shows that Amashito and Ojo de cangrejo (parents with a
greater phylogenetic relationship) were grouped first,
followed by Jalapeño and finally Habanero.
In conclusion, this study shows that molecular analyses
with AFLP markers are useful to estimate the
heterozygosity in chilli, as a good level of polymorphism
was detected in the tested materials. Genetic distances
based on DNA fragments obtained with molecular
markers for parents and their progeny were separated in
a well defined manner for germoplasm, according to their
respective species (parents and crosses), into both C.
annuum and C. chinense Jacq, confirming the genomic
differences between the two species. Besides, AFLP
markers are powerful tools for describing similarities
among the studied parents and their progenies. In
addition, it is concluded that genetic distances between
cultivars may be useful in choosing the best crosses to
obtain new pepper cultivars.