Classification and identification of bunching onion (Allium fistulosum) varieties based on SSR markers

We investigated the correspondence between classifications based on simple sequence repeat (SSR) markers and on morphological traits for 30 bunching onion (Allium fistulosum L.) varieties. We also examined applicability of an assignment test for variety identification in bunching onion. Cluster analysis based on the allele frequency data at 29 SSR loci classified most of the varieties except for 'Iwatsuki-2' into the predicted variety groups, 'Kaga', 'Senju' or 'Kujo', which were categorized based on morphological traits. Although 'Iwatsuki-2' has been regarded as a member of 'Kaga' group, molecular data suggested the variety belonging to 'Kujo' rather than 'Kaga'. In the assignment test at the individual level, 89.1% of the individuals were assigned to their original variety. When the assignment was conducted based on groups each consisting of four individuals, the percentage of correct assignments was considerably improved (99.3%). These results suggested that the assignment test approach will be useful for variety identification in allogamous bunching onions, which have large within-variety genetic diversity. On the other hand, it was also suggested that sampling of true source varieties will be fundamental to avoid misjudgment.