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Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: QTL mapping

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Abstract

The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over the first 4 years of growth of an apple F1 progeny by means of quantitative traits loci (QTL) mapping. Both growth and branching processes were phenotyped on the consecutive annual shoots of different axes within a tree. For each studied trait, predicted values (best linear unbiased predictors, BLUPs) of the genotypic (G) effect or its interaction with tree age (G×A) and climatic year (G×Y) were extracted from mixed linear models of repeated data. These BLUPs, which are independent from autocorrelations between repeated measurements, were used for QTL mapping. QTL detection power was improved by this two-step approach. For each architectural process, numerous QTLs were detected and some particularly interesting co-localised in common genomic regions, for internode lengthening, top diameter, and number and percentage of axillary shoots. When several QTLs were detected for a given trait, global models were estimated, which explained a maximum of 40% of the total variance for both internode length and top diameter and 28% for branching. QTLs detected for BLUPs of G×Y effects were interpreted as resulting from the interaction between genetic maximal potential of growth and climatic factors, while those for G×A effects were interpreted in relation to tree ontogeny. Most of the latter ones were found to be concomitant with key development stages during which the trait average started to decrease, but with different magnitudes depending on genotype.

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Acknowledgements

We acknowledge Mark Jones for improving the English. This research was partly funded by a grant from the INRA genetic and plant breeding department and Languedoc-Roussillon region, allocated to Vincent Segura.

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Authors and Affiliations

  1. INRA, UMR DAP, INRA–Montpellier SupAgro–CIRAD–Université Montpellier II, Equipe Architecture et Fonctionnement des Espèces Fruitières, 2 place P. Viala, 34060, Montpellier Cedex 1, France

    Vincent Segura & Evelyne Costes

  2. INRA, UMR GenHort, INRA–INH–Université d’Angers, 42 rue G. Morel, BP 57, 49071, Beaucouzé Cedex, France

    Charles-Eric Durel

Authors
  1. Vincent Segura
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  2. Charles-Eric Durel
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  3. Evelyne Costes
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Correspondence to Evelyne Costes.

Additional information

Communicated by A. Dandekar

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Figure S1

Genomic positions of QTLs detected on the linkage groups of the integrated ‘Starkrimson’ × ‘Granny Smith’ map for primary growth traits on the 123 genotypes replicated twice in the design planted in 2004. These data were analysed using a classic univariate approach without mixed linear modelling of repeated data, i.e. the data collected on the successive AS were analysed separately, and data collected on the different axes within a tree were not gathered to constitute the whole tree scale.QTLs are represented by boxes extended by lines representing the LOD-1 and LOD-2 confidence intervals. Triangle LOD peak. Boxes are coloured according to trait (GIF 68 kb)

High resolution image file (TIF 4283 kb)

Table S1

Correlations between BLUPs of (S1.a.) genotypic and age effects for mean internode length and (S1.b.) genotypic effect for mean internode length and length of the longest internode, and 2006 year effect for top diameter (DOC 108 kb)

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Segura, V., Durel, CE. & Costes, E. Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: QTL mapping. Tree Genetics & Genomes 5, 165–179 (2009). https://doi.org/10.1007/s11295-008-0181-x

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  • DOI: https://doi.org/10.1007/s11295-008-0181-x

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