Advanced genebank management of genetic resources of European wild apple, Malus sylvestris, using genome-wide SNP array data

The Netherlands' field genebank collection of European wild apple (Malus sylvestris), consisting of 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, and to develop a strategy to optimize the planting design of the collection as a seed orchard. We used the apple 20K Infinium single nucleotide polymorphism (SNP) array, developed in M. domestica, for the first time for genotyping in M. sylvestris. We could readily detect the clonal copies and unexpected duplicates. Thirty-two M. sylvestris accessions (29%) showed a close genetic relationship (parent-child, full-sib, or half-sib) to another accession, which reflects the small effective population size of the in situ populations. Traces of introgression from M. domestica were only found in 7 individuals. This indicates that pollination preferentially took place among the M. sylvestris trees. We conclude that the collection can be considered as mainly pure M. sylvestris accessions. The results imply that it should be managed as one unit when used for seed production. A bias in allele frequencies in the seeds may be prevented by not harvesting all accessions with a close genetic relationship to the others in the seed orchard. We discuss the value of using the SNP array to elaborate the M. sylvestris genetic resources more in depth, including for phasing the markers in a subset of the accessions, as a first step towards genetic resources management at the level of haplotypes.

Automated summary

The field genebank collection of European wild apple in the Netherlands was found to be mainly composed of pure M. sylvestris accessions, with about 29% of the accessions showing close genetic relationships. The study suggests that the collection should be managed as a single unit to prevent bias in allele frequencies in the seeds.