Genetic status of the Swedish central collection of heirloom apple cultivars

Cultivated apple is one of the most widely grown fruit crops worldwide. With the introduction of modern apple cultivars, from foreign and national breeding programs, the use of local cultivars decreased during the 20th century. In order to minimize genetic erosion and avoid loss of special genotypes, a number of local clonal archives were established across Sweden, with the goal of retaining old and local cultivars. About 220 apple cultivars, appointed for preservation, obtained the status of mandate cultivars. Initially, they were identified based on pomological traits, but prior to the establishment of the Swedish Central Collection they were genotyped with simple sequence repeat (SSR) markers. SSR markers helped to evaluate the status of the preserved material, as well as to find the best possible true-to-type source for propagation, thus guiding the establishment of the Central Collection. Recently, 215 accessions from this collection were genotyped using the 20 K apple Infinium® single nucleotide polymorphism (SNP) array, in order to gain insight into its genetic structure. The initial SSR analysis confirmed the identity of multiple samples with the same cultivar name grown in different locations and identified several mislabeled samples. In the subsequent SNP analysis we identified 30 clonal relationships and a number of parent-offspring relationships, including 18 trios. We also identified five cultivar samples with inconsistent ploidy levels between the SNP and SSR data, in some cases indicating problematic samples preserved in either the Central Collection or some of the local clonal archives. These cultivars need further investigation to ensure their true-to-typeness. Furthermore, the Swedish Central Collection has continued to grow since the onset of this work and now contains additional cultivars, which should be included in future studies. The results indicate that a number of the preserved mandate cultivars holds high potential value for modern breeding programs