DNA fingerprinting of apple (Malus spp.) rootstocks using Simple Sequence Repeats

Identification of apple clonal rootstocks based on visual morphological characteristics is often difficult because of the genetic similarity of many rootstocks and the restriction of observable characteristics at the nursery stage. In this study, a total of 66 rootstock clones representing a sub‐sample of a collection of apple rootstocks from different countries maintained at NIFTS, Morioka, Japan, was screened with seven simple sequence repeat (SSR) markers to establish genetic identities, estimate genetic diversity, verify parentage and examine genetic relationships. All seven SSR loci produced one or two amplified fragments and made it possible to differentiate among the rootstocks, except between virus‐free subclones and their original parents as well as between ‘Aotea 40’ and ‘Aotea 106’. The parentage of all but one rootstock clone was confirmed. The placement of individual rootstock clones into subgroups in a phenogram generated from un‐weighted pair group average cluster analysis was generally based on parentage or genetic origin. Based upon the ability of the SSR data to differentiate these apple rootstocks and the high level of gene diversity, it is proposed that all commercial apple rootstocks be fingerprinted to provide a mechanism to verify the identity of individual clones.