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

Published online by Cambridge University Press:  25 March 2014

Satish Kumar*
The New Zealand Institute for Plant and Food Research Limited, Private Bag 1401, Havelock North 4157, New Zealand
Pierre Raulier
Université Catholique de Louvain, 1348 Louvain-La-Neuve, Belgium
David Chagné
The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
Claire Whitworth
The New Zealand Institute for Plant and Food Research Limited, Private Bag 1401, Havelock North 4157, New Zealand
* Corresponding author. E-mail:


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< 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.

Research Article
Copyright © NIAB 2014 

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