title: A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation.
abstract: Systematic sequencing is the method of choice for generating genomic resources for molecular marker development and candidate gene identification in nonmodel 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.
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France.|Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France.|Helix Venture, F-33700, Mérignac, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Lesur
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France.|Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France.
authors.forename: Alison
authors.initials: A
authors.lastname: Bechade
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France.|Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Lalanne
authors.affiliation: Plateforme bioinformatique Genotoul, UR875UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326, Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: Plateforme bioinformatique Genotoul, UR875UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326, Castanet-Tolosan, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.affiliation: INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075, Orléans, France.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Leplé
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France.|Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Kremer
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France.|Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
authors.affiliation: INRA, UMR1202, BIOGECO, F-33610, Cestas, France.|Univ. Bordeaux, BIOGECO, UMR 1202, F-33615, Pessac, France.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Le Provost
mesh_terms: D005060:Europe; D020224:Expressed Sequence Tags; D029964:Fagus / Q000235:genetics* / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D056726:Genetic Association Studies; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D057445:Plant Dormancy; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
keywords: European beech; dormancy; molecular markers; qPCR; unigene