Evaluation of inter-species and in-species genetic variation of rye using AFLP molecular marker

Rye cereal Secale is one of the most important crops in Iran and belongs to the family Poaceae Understanding the Rye genetic diversity is essential for breeding programs of this plant. In this study, AFLP molecular markers were used to determine genetic diversity among 39 populations of Rye (from different regions of Iran, the United States and Russia). Thirteen primers were used, which could create 188 detectable and repeatable bands and 94% of primers showed polymorphism (177 bands) among different populations. The highest PIC was for the ECC 3N 4S 1 starter pair and the highest MI was for the ECC 3N 4S 5 starter pair. To determine the similarity between populations, the Dissse similarity coefficients were used. Maximum similarity (0.971) between the two populations Montanum of Park Jhan nama and Cereal of Fereydoun Shahr, and the minimum similarity (0.386) between Sermont of Arak and Sermont of the United States was observed. The cluster analysis was performed using the UPGMA algorithm based on the similarity matrix. Cluster analysis classified different populations of Rye in five main groups, which relevant to the grouping of principal components analysis. The results of this study showed noticeable genetic diversity among Rye populations of Iran, besides the results of the analysis of molecular variance show that intra-species diversity is higher than inter-species diversity, the average Shannon (I) index in rye species was 0.48, which indicates a relatively good diversity within species.