Molecular-level and trait-level differentiation between the cultivated apple (Malus X domestica Borkh.) and its main progenitor Malus sieversii

The present study is the first to compare the trait-level differentiation (Q(st)) and the molecular-level differentiation (F-st) between Malus X domestica and Malus sieversii. A set of 115 accessions representing M. X domestica (99) and M. sieversii (16) were genotyped using the International RosBREED SNP Consortium apple 8K SNP array and phenotyped for eight fruit quality traits in a clonally replicated experiment. A set of 3521 single nucleotide polymorphisms (SNPs) with an average call rate of 98% was retained following SNP data quality filters. About 86% of the total SNPs were polymorphic in M. sieversii, while all but three SNPs were polymorphic in M. X domestica. The patterns of linkage disequilibrium were different, especially at the longer distances, between the two species. No differentiation (F-st = 0) was observed for nearly 23% of the SNPs, but about 20% of the SNPs exhibited a high genetic differentiation (F-st >= 0.15). A highly significant (P < 0.001) genome-level F-st = 0.12 was observed between M. X domestica and M. sieversii. The average estimated Q(st) value was 0.20 (range 0.08-0.40), and for three of the eight studied traits (crispness, flavour intensity and fruit weight), Q(st) value was more than twice the estimated genome-level F-st value. A higher Q(st) value than F-st value for four of the eight fruit quality traits indicated differential (or directional) selection for these traits in M. X domestica. The average posterior probability of assignment of M. X domestica accessions to the M. sieversii gene pool was 11%, supporting the hypothesis of M. sieversii being one of the progenitors of the domesticated apple.