Molecular variability and genetic relationship and structure of Iranian Prunus rootstocks revealed by SSR and AFLP markers

Evaluation of genetic diversity in fruit trees requires fast, efficient and reliable techniques. The present study was undertaken to assess molecular variability, genetic relationship and population structure of 89 promising Prunus rootstocks and related parents from Iran. Results revealed that the average value of He detected by the SSR assay (0.80) was higher than that observed for AFLP (0.51). Moreover, SSR markers were found most polymorphic with the highest average PIC value (0.78) and marker index (1.87), suggesting that the SSR technique could be more informative than the AFLP method in genetic diversity studies. Neighbor-Net cluster analysis based on both SSRs and AFLPs divided Prunus germplasm into three and eight main clusters, respectively. The results revealed that the classification of Prunus samples on the basis of SSR loci seems to be more accordance with their genealogical data than AFLP. Also, the grouping obtained from Bayesian method were completely coincident with the grouping that we observed in the phylogenetic relatedness analysis, taking into account that the AFLP markers were more capable for analyzing the structure of Prunus populations than SSRs. Our data suggest that SSR marker as an effective tool for evaluation of relationships within germplasm and AFLP as a powerful technique in population structure experiments. The set of SSR and AFLP loci used in this study illustrated that the genetic base of the Iranian Prunus collection is broad enough to ensure future progress in breeding programs and the markers used in this research are potent methods to conduct diversity studies in candidate Prunus rootstocks and their parental species.