Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data

The domesticated apple (Malus domestica) is widely considered an admixture primarily involving M. sieversii, M. sylvestris, and M. orientalis, with possible contributions from tiny-fruited species such as M. baccata. Although this origin theory is well supported by genomic studies, the relative contributions of each progenitor species to cultivar genomes remain unclear, and taxonomic classifications of some Malus species are conflicting. The availability of new genomic tools and resources enables probing of these topics.

A panel of wild Malus accessions was genotyped using the Illumina Infinium 20K apple SNP array to generate a library of species-specific SNP and haploblock alleles. After excluding heavily admixed individuals and masking admixture haplotypes in individuals with small amounts of admixture, this library was used to clarify the ancestry of 436 wild accessions and estimate the genomic proportions attributable to M. sieversii, M. sylvestris, M. orientalis, and collectively, tiny-fruited Malus species in M. domestica cultivars. The results were broadly consistent with previous studies but revealed new ancestry details and enabled precise haplotype-level attributions. Previously unreported admixture and taxonomic irregularities were detected for some wild accessions. All M. domestica cultivars were found to be mixtures of the three primary progenitors, with some also showing contributions from tiny-fruited Malus species. The relative contributions varied among cultivars, with evidence that older cultivars and traditional cultivars originating in eastern Europe or Western Asia had less M. sylvestris ancestry than modern cultivars and traditional cultivars originating in Western Europe.

This study provides new insights into apple ancestry and highlights the need for clarification in Malus taxonomy. The findings have implications for germplasm management, historical research, and genetic improvement of apple cultivars. The species-specific allele library developed here offers a valuable resource for routine admixture estimation of Malus accessions genotyped on the same set of SNPs.