Use of SSR markers to assess sexual vs. apomictic origin and ploidy level of breeding progeny derived from crosses of apple proliferation-resistant Malus sieboldii and its hybrids with Malus x domestica cultivars

To obtain apple rootstocks resistant to apple proliferation and suitable to modern fruit growing, 24 cross-combinations were performed over a 5-year period using Malus sieboldii and its hybrids as donors of the resistance trait and standard apple rootstock Malus x domestica genotypes as donors of agronomic value. Breeding with these genotypes was achieved despite different degrees of apomixis and polyploidy. Sets of five to six locus-specific microsatellite markers were identified for characterizing each progeny. Supported by flow cytometry these markers were applied to infer mode of reproduction, genomic constitution and ploidy level. Microsatellites allele composition identical to the maternal parent was revealed in 1668 of 3032 seedlings indicating seed formation through apomixis. Complete genetic recombination was found in 398 seedlings. The remaining hybrids displayed a higher ploidy than that of the parental plants which was consistent with the fertilization of unreduced egg cells. Thus, for each cross-combination, microsatellite loci were identified which enabled a reliable prediction of the ploidy level. They can now be applied in routine screening to distinguish sexual from apomictic progeny.