Genetic variability and population genetic structure in autotriploid saffron using allelic phenotypes of microsatellite markers

Abstract

A comprehensive effort was made to characterize potential inter- and intra-population genetic variation governing on the saffron ecotypes originating from 18 distinct geographical regions of Iran (90 accessions) using “allelic phenotypes” of 16 microsatellite markers. The 11 SSR loci (69%) that were polymorphic across the 90 saffron genotypes produced 30 alleles, of which ABRII/CS2 was the most informative locus. Both PCoA and UPGMA phylogenetic tree, alongside Bayesian model-based clustering grouped the 18 ecotypes into three major groups, with similar classification patterns, and highly consistent with geographical distribution. The assignment test accurately assigned 83 out of 90 saffron accessions (92.22%) to the corresponding populations, while the remainder were placed in adjacent populations. The AMOVA results revealed a high level of genetic variation within saffron populations (>80%), with a small fraction among populations (<20%). For the entire 90 accessions, significant correlation was detected between genetic and geographical distances (Mantel test, r = 0.173; P = 0.038). The results, overall, indicated the efficacy of allelic phenotypes-assisted DNA fingerprinting approach in making discrimination and unraveling potential genetic diversity among various Iranian saffron ecotypes, and possibly other autopolyploid crops.