Cleavage Amplification Polymorphism (CAP) technique was used to detect chloroplast DNA (cpDNA) diversity in 26 Iranian apple genotypes (19 from Azerbaijan) as well as two commercial cultivars and two dwarf rootstocks. Study of approximately 4.13% of the total chloroplast genome by using three chloroplast universal primer pairs and two restriction enzymes (EcoR I and Mse I) detected 8 haplotypes. The most-abundant and widely distributed haplotype was H4 (frequency = 26.66% approximately). Three haplotypes (H1, H3 and H6) were exclusive haplotypes of Azerbaijan population. All the mutations detected were insertion-deletions in the range of 20 to 50 bp. The total cpDNA diversity in populations was hT=0.467, and a major portion of it was within populations (hS=0.445). The genetic differentiation among populations was low (GSTC=0.048) and no genetic structure was observed. This result proposes the possible utilization of the CAP technique for the characterization of apple genotypes and cultivars. The polymorphism in cpDNA of Malus has to be considered carefully when planning phylogenetic studies involving this species.
Key words: Malus, chloroplast DNA (cpDNA), haplotype, cleavage amplification polymorphism (CAP), chloroplast universal primerc, restriction enzymes, phylogenetic.
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