Exploring the population structure and genetic diversity in apple germplasm using iPBS-retrotransposon markers

The apple (Malus domestica [Suckow] Borkh) is economically and culturally significant worldwide, thriving in temperate regions. This study examined genetic variations among 52 apple accessions from three research centers in Kazakhstan using the iPBS-retrotransposons marker system. Out of 35 screened markers, 12 highly polymorphic markers were selected for PCR amplification, resulting in 280 bands, 279 of which were polymorphic, yielding a 99.64% polymorphism rate. Genetic diversity indices showed substantial variation: effective number of alleles (ne=1.655), Shannon's information index (I=0.373), gene diversity (h=0.549), and an average genetic distance of 1.2. The analysis of molecular variance (AMOVA) indicated that 98.80% of the variation was within the population. STRUCTURE analysis grouped the germplasm into two populations and one unclassified group based on collection centers. Both the neighbor-joining tree and PCoA supported the STRUCTURE results, dividing the germplasm into two groups. The study highlighted significant genetic variation among apple accessions, demonstrating the effectiveness of the iPBS-retrotransposons marker system. The STRUCTURE analysis provided clearer separation of accessions compared to neighbor-joining trees. The highest genetic distance of 1.2 was observed between the Tyulpan and Red Chief samples, making these accessions suitable candidates for advanced breeding initiatives.