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Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population

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Abstract

Association mapping is a recommended method to dissect the genetic basis of naturally occurring trait variation in non-model tree species with outcrossing mating systems and large population sizes. We report here the results of the first association-mapping study in maritime pine (Pinus pinaster Ait.), a conifer species of economical importance for timber and pulp production in south-western Europe. Two association samples were examined: 160 plus trees belonging to the first generation breeding population (G0, resulting from mass selection for overall good growth and form in the forest of South West of France) and 162 trees from the second generation breeding population (G1, resulting from biparental crosses between G0 trees). These samples were (1) genotyped for 184 in vitro SNPs discovered in 40 candidate genes for plant cell wall formation or drought stress resistance and 200 in silico SNPs detected in 146 contigs from the maritime pine EST database and (2) phenotyped for growth, stem straightness and wood chemistry traits in progeny or clonal experimental designs (from 768 to 5,080 phenotypes depending on the trait). First, SNP data were used to test for putative stratification in the breeding population. Then, two different approaches using pedigree records to account for inbreeding were used to test for associations. Despite the a priori low power of the designs, we identified two mutations that were significantly associated, one with variation in growth (in a HD-Zip III transcription factor) and the other with variation in wood cellulose content (in a fasciclin-like arabinogalactan protein).

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Acknowledgements

This research was supported by grants from Agence Nationale de la Recherche: Genoplante (GenoQB, GNP05013C), Agence Nationale de la Recherche ‘Plates-Formes Technologiques du Vivant’ (BOOST-SNP, 07PFTV002), the Aquitaine Region (20061201004PFM), the European Union (NOVELTREE project, FP7-211868) and the EVOLTREE Network of Excellence (contract number 016322). C. Lepoittevin was supported by CIFRE contract between FCBA and INRA. The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. INRA, UMR1202 BIOGECO, 33610, Cestas, France

    Camille Lepoittevin, Christophe Plomion & Pauline Garnier-Géré

  2. Université de Bordeaux, UMR1202 BIOGECO, 33400, Talence, France

    Camille Lepoittevin, Christophe Plomion & Pauline Garnier-Géré

  3. FCBA, Laboratoire de Biotechnologies, 77370, Nangis, France

    Camille Lepoittevin & Luc Harvengt

Authors
  1. Camille Lepoittevin
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  2. Luc Harvengt
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  3. Christophe Plomion
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  4. Pauline Garnier-Géré
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Correspondence to Camille Lepoittevin.

Additional information

Communicated by S. Aitken

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online resource 1

Geographic origin of the G0 trees (table of coordinates and map) (PDF 315 kb)

Online resource 2

Results of the Structure analysis on the 160 G0 samples (a, b) and on the 28 unrelated G1 samples (c, d). a, c Mean likelihood L(K) and its standard error over 10 runs of the Structure software for each number of subpopulations K. b, d Evanno criterion ∆K for each K value (the y-scale is chosen for the criteria to be informative as in Evanno et al. 2005) (PDF 105 kb)

Online resource 3

Hierarchical clustering dendrograms obtained by the H-clust method (Rinaldo et al. 2005) for the 160 G0 samples (a) and the 28 unrelated G1 samples (b). The cut-off value is indicated by a dashed line and the informative SNPs by a star. In each block, the selected SNP is chosen as the SNP most correlated with all the other SNPs in the block. If several SNPs are equivalent, the one showing the lower number of missing data is selected (PDF 396 kb)

Online resource 4

P values, q values and P′ values for the SNP effect in the additive model, for 141 informative SNPs in the G0 samples (list of SNPs and values of test statistics available in Online resource 5) (JPEG 1562 kb)

High resolution (EPS 116 kb)

Online resource 5

Table of P values, q values, P′ values and heritabilities for the association tests in the G0 and G1 populations (XLS 319 kb)

Online resource 6

Distribution of P values for the codominant (a) and additive (b) models for Diameter in the G1 sample. a There is no plateau in the distribution, thus the proportion of null P values cannot be estimated by the empirical method (Storey and Tibshirani 2003) and the ad hoc estimation produces very low q values (see Fig. 4). b There is a plateau in the distribution that allows estimating the proportion of null P values, which is close to 0.5 (PDF 7 kb)

Online resource 7

Power of single-marker-based association tests as a function of SNP minor allele frequency and heritability, for a 10−5 alpha threshold and a sample size of 1,000 (a) or 160 (b) individuals. Power was calculated using the ldDesign package (Ball 2004), assuming that the SNP considered was the causative mutation (implemented in the ldDesign package by setting the linkage disequilibrium D value to its maximum) and that the genotypic frequencies followed Hardy–Weinberg equilibrium (PDF 139 kb)

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Lepoittevin, C., Harvengt, L., Plomion, C. et al. Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population. Tree Genetics & Genomes 8, 113–126 (2012). https://doi.org/10.1007/s11295-011-0426-y

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  • DOI: https://doi.org/10.1007/s11295-011-0426-y

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