In order to separate samples in Group I from AFLP analysis, data from AFLP and MSAFLP
analyses were combined and analyzed together to elucidate the effects of methylationsensitive
data to tree topology. After excluding the samples of JCL25, JCL26 and non-toxic
accessions, which were clearly separated according to AFLP and MS-AFLP phylogenetic tree,
the combination data were analyzed for genetic similarity based on Sneath and Sokal (1973)
and a phylogenetic tree was constructed using the UPGMA method. All 49 JCL samples in
Group I of the AFLP analysis were clearly separated into 5 subgroups at a genetic similarity
of 0.972 (Figure 1C). The cophenetic correlation coefficient revealed a good fit of cluster
analysis, with a value of r = 0.81 for the dendrogram. Interestingly, the hybrid from Anna21
and E-L23 (JCL23) was separated from the major group independently. Genetic similarity
estimated by Sneath and Sokal (1973) among samples studied was extremely high, ranging
from 0.96 to 1.00. Principal components 1, 2 and 3 accounted for 80.98, 4.70 and 2.94% of
total variation, respectively.