Assessment of genetic diversity and genetic relationships among 46 Iranian and non-Iranian dwarfing rootstocks of apple (Malus × domestica Borkh.) using microsatellite markers

Abstract

SummaryDwarfing apple rootstocks are essential in modern apple production for the control of vigour, increased disease resistance, precocity, and predictability in orchard management. Such rootstocks also decrease the cost of production by lowering the costs of pruning, spraying, and harvesting. In this study, 18 new microsatellite (simple sequence repeat; SSR) markers were isolated and identified from a repeat sequence-enriched genomic library of Iranian dwarfing apple rootstocks using a modified Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) procedure. GA/GT and AG repeat motifs were the most abundant di-nucleotides isolated. Nineteen microsatellite markers from previous work were also chosen for analysis in this study. Thirty-seven microsatellite markers, in total, were thus used to evaluate the genetic structure and genetic diversity of 46 individual (34 Iranian and 12 others) dwarfing apple rootstocks. In total, 187 polymorphic bands were generated, with an average of 5.05 alleles per locus. Averages values of the key parameters among all samples tested were: Shannon’s Index, 1.23; observed heterozygosity (Ho), 0.53; expected heterozygosity (He), 0.63; and inbreeding between sub-populations, 0.17. The polymorphic information content (PIC) varied from 0.31 – 0.70. Neighbor-Net analysis divided the dwarfing apple rootstocks into five groups. Approx. 91% of the Iranian dwarfing apple rootstocks had a different genetic structure and higher diversity than the non-Iranian rootstocks. All SSR motifs identified in this study, including the new SSRs, will be useful resources for genetic studies in apple and for comparative genomic studies in other members of the Rosaceae.