Molecular-level and trait-level differentiation between the cultivated apple (<i>Malus</i>× <i>domestica</i>Borkh.) and its main progenitor<i>Malus</i><i>sieversii</i>

Abstract

The present study is the first to compare the trait-level differentiation ( Q st ) and the molecular-level differentiation ( F st ) between Malus × domestica and Malus sieversii . A set of 115 accessions representing M. × 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. × 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 &lt; 0.001) genome-level F st = 0.12 was observed between M. × 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. × domestica . The average posterior probability of assignment of M. × 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.