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QTL and candidate gene mapping for polyphenolic composition in apple fruit

David Chagné1*, Célia Krieger12, Maysoon Rassam3, Mike Sullivan3, Jenny Fraser4, Christelle André3, Massimo Pindo5, Michela Troggio5, Susan E Gardiner1, Rebecca A Henry3, Andrew C Allan36, Tony K McGhie1 and William A Laing3

Author affiliations

1 The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand

2 UMR 1121 Nancy Université-Institut National de la Recherche Agronomique Agronomie Environnement Nancy-Colmar, 2 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France

3 Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand

4 Plant & Food Research, Central Otago Research Centre, Clyde, New Zealand

5 IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy

6 School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand

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Citation and License

BMC Plant Biology 2012, 12:12  doi:10.1186/1471-2229-12-12

Published: 23 January 2012



The polyphenolic products of the phenylpropanoid pathway, including proanthocyanidins, anthocyanins and flavonols, possess antioxidant properties that may provide health benefits. To investigate the genetic architecture of control of their biosynthesis in apple fruit, various polyphenolic compounds were quantified in progeny from a 'Royal Gala' × 'Braeburn' apple population segregating for antioxidant content, using ultra high performance liquid chromatography of extracts derived from fruit cortex and skin.


Construction of genetic maps for 'Royal Gala' and 'Braeburn' enabled detection of 79 quantitative trait loci (QTL) for content of 17 fruit polyphenolic compounds. Seven QTL clusters were stable across two years of harvest and included QTLs for content of flavanols, flavonols, anthocyanins and hydroxycinnamic acids. Alignment of the parental genetic maps with the apple whole genome sequence in silico enabled screening for co-segregation with the QTLs of a range of candidate genes coding for enzymes in the polyphenolic biosynthetic pathway. This co-location was confirmed by genetic mapping of markers derived from the gene sequences. Leucoanthocyanidin reductase (LAR1) co-located with a QTL cluster for the fruit flavanols catechin, epicatechin, procyanidin dimer and five unknown procyanidin oligomers identified near the top of linkage group (LG) 16, while hydroxy cinnamate/quinate transferase (HCT/HQT) co-located with a QTL for chlorogenic acid concentration mapping near the bottom of LG 17.


We conclude that LAR1 and HCT/HQT are likely to influence the concentration of these compounds in apple fruit and provide useful allele-specific markers for marker assisted selection of trees bearing fruit with healthy attributes.

Malus x domestica; polyphenolic; QTL mapping; candidate gene; flavonoid; flavanol; anthocyanin; tannin; metabolomics