Genetic diversity, structure, and core collection of Korean apple germplasm using simple sequence repeat markers

An apple (Malus × domestica Borkh.) core collection was established using 19 SSR markers in 1,344 apple germplasm samples using the PowerCore program. For this, 166 accessions were selected using a heuristic strategy, accounting for about 12.4% of the entire collection. The core collection had an allelic loci retention ratio of 100%, and no significant differences were observed in the number of alleles, Shannon’s information index, observed heterozygosity, expected heterozygosity, major allele frequency, or polymorphic information content between the core and the entire collection, as indicated by t-tests and Levene’s test. Analysis of molecular variance also revealed no significant genetic variation between the core and the entire collection. For all apple accessions, the genetic relationship, assessed using neighbor-joining analysis, was divided into five clusters, and the population structure had the highest value at k = 2. The first two axes in the principal coordinate analysis accounted for 14.00% and 9.85% of the total variance, and the core collection was distributed in a scattered pattern across the plot of the entire collection. The 166-apple core set constructed here is recommended for use as the core collection for the Korean apple germplasm.