Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Analysis Of Expressed Sequence Tags In Maritime Pine (Pinus pinaster Ait)

Grégoire Le Provost¹ , Philippe Chaumeil¹ , Jean-Marc Frigèrio¹ , jorge Paiva^1,2 , Patrick Léger¹ , franck Salin¹ , Maite Cervera³ , Nacer Mohellibi⁴ , Francisco Canton⁵ , Christophe Plomion¹

¹  UMR BIOGECO, INRA 69 route d'Arcachon 33610 CESTAS, France

²  Plant Cell Biotechnology Lab. IBET/ITQB, Quinta do Marques 2780 Oeiras,Portugal.

³  Departamento de Genética Forestal, CIFOR-INIA, Carretera de la Coruna Km 7, 28040 Madrid, Spain

⁴  Centre de Bioinformatique de Bordeaux, Plateforme Génomique fonctionnelle Bordeaux, Université Bordeaux 2, 33076 Bordeaux, France.

⁵  Biología Molecular y Bioquímica, Facultad de Ciencias e Instituto Andaluz de Biotecnología ,Unidad Asociada UMA-CSIC, Campus Universitario de Teatinos, Universidad de Málaga, E-29071 Málaga, Spain

Maritime pine is a foreground species for the forestry wood chain in South-Western Europe. A breeding program of this species started half a century ago and has now reach its third generation. Early indirect selection criteria are now being investigated to develop varieties with improved wood quality and adapted to more limited water resource. In this context, molecular markers and genes in particular, offer diagnostic tools of choice, given that they are link to trait variation. With the main objective of discovering economically and ecologically important genes, we developed an EST resource for this species. Four cDNA libraries were constructed using RNA extracted from different tissues (needles, roots, differentiating xylems and buds). A mean of 10,000 sequencing runs were performed per library (except for the needles where only 700 runs were performed). Unexploitable chromatogram and quality checking lead us to eliminate 7,000 sequences (20%). Finally, 26,669 EST were obtained and used in the assembly step (stackPACKTM softwear avalaible at http://www.sanbi.ac.za). Of the 26,669 sequences, 19,271 sequences were members of one of the 4,132 primary consensus found with 7,358 remaining as singletons corresponding to a redundancy of 70%. A functional annotation (gene function and metabolic classification) was then assigned to each consensus and singleton. This genomic resource provide a tool to study the maritime pine transcriptome and investigate functional diversity in natural population.