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

Apple ( Malus domestica [Suckow] Borkh) holds global economic and cultural value, particularly in temperate regions. This study investigates the genetic variations among 52 apple accessions from three research centre's in Kazakhstan, employing the iPBS-retrotransposons marker system. Of the 35 markers initially screened, 12 highly polymorphic markers were selected for PCR amplification, producing 280 bands, 279 of which were polymorphic, yielding a polymorphism rate of 99.64%. Genetic diversity indices revealed notable variability with the 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. Analysis of molecular variance (AMOVA) demonstrated that 97% of the genetic variation occurred within the population. STRUCTURE analysis divided the germplasm into two distinct populations and one unclassified population based on collection centers. Both the neighbor-joining tree and principal coordinate analysis (PCoA) supported these results, confirming the genetic separation into two groups. This study highlighted the significant genetic diversity among apple accessions, demonstrating the effectiveness of the iPBS-retrotransposons marker system. Additionally, the highest genetic distance (1.2) observed between the Tyulpan and Red Chief samples, positions these accessions as suitable and promising candidates for future breeding initiatives.