Compared to other Polymerase Chain Reaction (PCR) based molecular markers, the Amplified Fragment Length Polymorphism (AFLP) marker system probably requires more technical expertise for the sequential enzymatic reaction steps. In addition, the reproducibility of the AFLP marker patterns is much more dependent on the quality and the purity of the DNA samples to be processed. The present study describes the optimization of reaction conditions and determination of the most polymorphic selective amplification primer sets in a comparison of winter and spring type Turkish durum wheat varieties. AFLP products resulted in about 100 bands, and the number of polymorphic AFLP loci obtained ranged from 6 to 32 per selective primer combination. Among the nine Aegilops accessions, at a single combination, 137 polymorphic loci were observed.

Compared to other Polymerase Chain Reaction (PCR) based molecular markers, the Amplified Fragment Length Polymorphism (AFLP) marker system probably requires more technical expertise for the sequential enzymatic reaction steps. In addition, the reproducibility of the AFLP marker patterns is much more dependent on the quality and the purity of the DNA samples to be processed. The present study describes the optimization of reaction conditions and determination of the most polymorphic selective amplification primer sets in a comparison of winter and spring type Turkish durum wheat varieties. AFLP products resulted in about 100 bands, and the number of polymorphic AFLP loci obtained ranged from 6 to 32 per selective primer combination. Among the nine Aegilops accessions, at a single combination, 137 polymorphic loci were observed.