Validation of criteria for the selection of AFLP markers to assess the genetic variation of a breeders' collection of evergreen azaleas

Fluorescent AFLP and automated data analysis were employed to assess the ge netic conformity within a breeders' collection of evergreen azaleas. The st udy included 75 genotypes of Belgian pot azaleas (Rhododendron simsii Planc h. hybrids), Kurume and Hirado azaleas and wild ancestor species from the T sutsusi subgenus. Fluorescent detection and addition of an internal size st andard to each lane enabled the automated scoring of each fragment arising from a single AFLP primer combination (PC), The use of three PCs generated an initial data set with a total of 648 fragments ranging from 70 bp to 450 bp. Different marker selection thresholds for average fluorescent signal i ntensity and marker frequency were used to create eight extra restricted da ta subsets. Pairwise plant genetic similarity was calculated for the nine d ata sets using the Simple Matching coefficient (symmetrical, including doub le-zeros) and Jaccard coefficient (asymmetrical, excluding double zeros). T he averages, the ranges and the correlation to one other (Mantel analysis) were compared for the obtained similarity matrices. This revealed the sensi tivity of ordinations obtained by both similarity coefficients for the pres ence of weak or intensive markers or for the degree of polymorphism of the markers. For 34 cultivars, pedigree information (at maximum to the fifth an cestor generation) was available. Genetic similarity by descent (kinship co efficient) was turned into a genetic distance and correlated to the genetic conformity, as revealed by the different selections of AFLP markers (Mante l analysis). Use of a Simple Matching coefficient with no or moderate selec tion to signal intensity and excluding rare and abundant markers gave the b est correlation with pedigree. Finally, the ordination of the studied genot ypes by means of dendrograms and principal co-ordinate analysis was confron ted with known or accepted relationships based on geographical origin, pare ntage and morphological characters. Genotypes could be assigned to three di stinct groups: pot azaleas, Kurume azaleas and Hirado azaleas, Wild ancesto r species appeared to be more related to the Japanese azaleas, Intermediate cultivars could be typified as crossings with Kurume or Hirado azaleas or with wild species.