A unigene set for European beech ( Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulationby Isabelle Lesur, Alison Bechade, Céline Lalanne, Christophe Klopp, Céline Noirot, Jean-Charles Leplé, Antoine Kremer, Christophe Plomion, Grégoire Le Provost

Molecular Ecology Resources

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Year
2015
DOI
10.1111/1755-0998.12373
Subject
Ecology, Evolution, Behavior and Systematics / Biotechnology / Genetics

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This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1755-0998.12373

This article is protected by copyright. All rights reserved.

Received Date : 03-Nov-2014

Revised Date : 06-Jan-2015

Accepted Date : 13-Jan-2015

Article type : Resource Article

A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation.

Isabelle Lesur 1,2,3 , Alison Bechade 1,2 , Céline Lalanne 1,2 , Christophe Klopp 4 , Céline Noirot 4 ,

Jean-Charles Leplé 5 , Antoine Kremer 1,2 , Christophe Plomion 1,2 and Grégoire Le Provost 1, 2, † 1

INRA, BIOGECO, UMR 1202, F-33610 Cestas, France. 2

Univ. Bordeaux, BIOGECO, UMR 1202, F-33400 Talence, France. 3

Helix Venture, F-33700 Mérignac, France. 4

Plateforme bioinformatique Genotoul, UR875UR875 Mathématique et Informatique

Appliquée de Toulouse, INRA, 31326 Castanet-Tolosan, France. 5

INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075 Orléans,

France.

Keywords: European beech, unigene, dormancy, molecular markers, qPCR. †

Corresponding author: Gregoire Le Provost

INRA, BIOGECO, UMR 1202, F-33610 Cestas, France.

Tel: +33(0)557122773,

Fax: +33(0)557122881 e-mail: leprovost@pierroton.inra.fr

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Running Head: A unigene set for European beech

Abstract

Systematic sequencing is the method of choice for generating genomic resources for molecular marker development and candidate gene identification in non-model species. We generated 47,357 Sanger ESTs and 2.2M Roche-454 reads from five cDNA libraries for

European beech (Fagus sylvatica L.). This tree species of high ecological and economic value in Europe is among the most representative trees of deciduous broadleaf forests. The sequences generated were assembled into 21,057 contigs with MIRA software. Functional annotations were obtained for 85% of these contigs, from the proteomes of four plant species,

Swissprot accessions and the Gene Ontology database. We were able to identify 28,079 in silico SNPs for future marker development. Moreover, RNAseq and qPCR approaches identified genes and gene networks regulated differentially between two critical phenological stages preceding vegetative bud burst (the quiescent and swelling buds stages). According to climatic model based projection, some European beech populations may be endangered, particularly at the southern and eastern edges of the European distribution range, which are strongly affected by current climate change. This first genomic resource for the genus Fagus should facilitate the identification of key genes for beech adaptation and management strategies for preserving beech adaptability.

Introduction

European beech (Fagus sylvatica) is one of the most widespread forest trees in Europe, with a natural distribution range of more than 300,000 km² extending from Sicily to southern

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Sweden (Leuschner et al. 2006). Beech is a major timber species, essential to the maintenance of European forest diversity and providing diverse ecosystem services. The area covered by beech has increased steadily in recent decades. This species plays a key role in the current shift from intensely managed plantation forests towards largely self-regenerating mixed broadleaf stands (Geßler et al. 2007). However, current species distribution models predict a marked shift in the potential distribution range of this species by 2100 (Cheaib et al. 2012). The predictive models used by this author agree with a substantial contraction of beech area in the southern and central part of France associated to an upward shift of 100200m in the mountains.

An understanding of the adaptive potential of beech populations is essential, given their key role in forest ecosystem functioning. Phenology is strongly affected by global warming (Chuine & Cour 1999). Vegetative bud phenology is particularly important, because the duration of the growing season (determining the annual production of forest trees) depends on the length of time between bud burst in spring and bud set in autumn, which is determined largely by temperature. A better comprehension of the physiological and molecular mechanisms underlying switches between bud phenological stages (i.e dormancy regulation) are therefore essential, to improve our understanding and forecasting of beech performance in conditions of climate change.

European beech and the other ten Fagus species belong to the Fagaceae family, which includes about 900 evergreen and deciduous tree and shrub species. Abundant genomic resources are available only for Quercus (oaks) and Castanea (chestnuts), including a geneatlas (Ueno et al. 2010; Barakat et al. 2012; Tarkka et al. 2013), SNP catalogs (Lepoittevin et al. in preparation), BAC libraries and physical maps (Faivre Rampant et al. 2011; Fang et al. 2013), gene-based linkage maps (Bodénès et al. 2012; Kubisiak et al. 2013)

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This article is protected by copyright. All rights reserved. and genome sequences (Plomion & Fievet 2013). Gene and protein expression studies have also been performed, to identify the key molecular players in vegetative bud phenology (Derory et al. 2006; Ueno et al. 2013) and responses to biotic and abiotic stresses, such as

Cryphonectria parasitica (Barakat et al. 2012), Tortrix viridina (Kersten et al. 2013) and waterlogging (Le Provost et al. 2011). Forward genetic approaches (QTL and association mapping studies) to dissecting the genetic architecture of adaptive traits and identifying genes/polymorphisms important for adaptation (Kremer et al. 2012) have also benefited from these tools. However, the genomic resources available for Fagus remain limited. A single genetic map has been generated (Scalfi et al. 2004), through the use of RAPD, AFLP and