Genomic diversity in date palm (Phoenix dactylifera L.) as revealed by AFLPs in comparison to RAPDs and ISSRs

Fourteen date palm (Phoenix dactylifera L.) accessions collected from different locations in Egypt representing six Egyptian cultivars: Sakkoty, Bertmoda, Malkaby, Gandila, Fraihy and Siwi were assayed using 16 AFLP primer combinations. AFLP analysis generated a total of 657 amplicons representing a level of polymorphism of 45.8%. The genetic similarity and relationships were estimated among the 14 accessions and among the six cultivars according to Dice coefficient.The AFLP-based dendrograms clustered the genotypes of some cultivars together, i.e. Fraihy and Gandila. The genotypes of Siwi cultivar were clustered together also, but they exhibited some degree of intravarietal variation. The other three cultivars (Sakkoty, Bertmoda, and Malkaby) showed higher degree of intravarietal variation. Moreover, at the intervarietal level, the AFLP assay separated the oases cultivars i.e., Siwi and Fraihy, from the cultivars from Aswan, i.e. Sakkoty, Bertmoda, Malkaby and Gandila. AFLP analysis permitted the characterization of each cultivar by specific unique markers.Data from RAPD’s and ISSR’s, previously obtained on the same 14 accessions were combined with AFLP’s to generate more accurate relationships based on large and versatile genome coverage. The dendrogram based on the combined data from the different types of markers (RAPD, ISSR and AFLP) was closest to the AFLP-based dendrogram. To evaluate the efficiency of the different marker systems, the sum effective number of alleles (SENA), the average expected heterozygosity for polymorphic markers (Hav(p)), the effective multiplex ratio (E) and marker index (MI) were calculated. The AFLP exhibited considerably high sum effective number of alleles (205.7) compared to RAPD and ISSR (45.1 and 17.8, respectively). The average heterozygosity was also higher in AFLP (0.39) than in RAPD and ISSR (0.36 and 0.35, respectively). The MI was 117.3 in AFLP while it was 95.9 and 10.4 in RAPD and ISSR, respectively. Thus, the results indicated that AFLP is more effective in detecting high level of polymorphism. The correlation coefficient was considerably high between RAPD and ISSR (0.68), and it was lower between RAPD and AFLP (0.23) than that between AFLP and ISSR (0.34). The results confirmed that different marker systems differ in the mechanism of detecting polymorphism, genome coverage and the ease of application. Therefore, they could complement each other to draw more accurate conclusions.