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Open Access Research article

Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

Yung-Fen Huang12, Agnès Doligez1*, Alexandre Fournier-Level15, Loïc Le Cunff13, Yves Bertrand1, Aurélie Canaguier4, Cécile Morel1, Valérie Miralles1, Frédéric Veran2, Jean-Marc Souquet2, Véronique Cheynier2, Nancy Terrier2 and Patrice This1

Author Affiliations

1 UMR AGAP, INRA, 2, place Viala, 34060 Montpellier, France

2 INRA, UMR1083 SPO, 2, place, Viala, 34060 Montpellier, France

3 UMT Geno-Vigne®, IFV, 2, place Viala, 34060 Montpellier, France

4 UMR Génomique Végétale, INRA UEVE ERL CNRS, 2, rue Gaston Crémieux, 91057 Evry, France

5 Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G-W, Providence, RI 02912, USA

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BMC Plant Biology 2012, 12:30  doi:10.1186/1471-2229-12-30

Published: 27 February 2012

Abstract

Background

Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs.

Results

Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel.

Conclusions

This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.