For all pair-wise comparisons of GS estimates, GSAFLP ranged from 0.73 to 0.99
with an average of 0.88. GSSSR ranged from 0 to 0.74 with an average of 0.25.
Accessions PHA346, PHA374, and ‘MDRK’ shared no SSR allele with accession
PHA717. The Mantel test for comparison of the AFLP-based and SSR-based
similarity matrices showed moderate but significant correlation (r = 0.69).
The dendrograms generated with hierarchical UPGMA cluster analysis of the
Jaccard’s similarity coefficient matrices revealed two major clusters with 100%
bootstrap values (Figure 1). The cophenetic correlation between the dendrogram
and the similarity matrix was moderate for SSR (r = 0.82) and high for AFLP (r =
0.96). Cluster I contained Andean check accession ‘MDRK’ and 23 Slovene
accessions distributed into two sub-clusters, Sub-cluster I and Sub-cluster II. In
addition to Mesoamerican check accession ‘Michelite’, minor Cluster II contained
only four Slovene accessions. Two accessions, PHA438 and PHA346, clustered
differently in dendrograms, and these deviations appeared only on the level of the sub-clusters. Cophenetic correlation of AFLP-based and SSR-based cophenetic
matrices was moderate (r = 0.78) but highly significant.