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Forest Tree Genomics Forest tree genomics: 10 achievements from the past 10 years and future prospects Christophe Plomion, Catherine Bastien, Marie-Béatrice Bogeat-Triboulot, Laurent Bouffier, Annabelle Déjardin, Sébastien Duplessis, Bruno Fady, Myriam Heuertz, Anne-Laure Le Gac, Grégoire Le Provost, et al. To cite this version: Christophe Plomion, Catherine Bastien, Marie-Béatrice Bogeat-Triboulot, Laurent Bouffier, Annabelle Déjardin, et al.. Forest tree genomics: 10 achievements from the past 10 years and future prospects. Annals of Forest Science, Springer Nature (since 2011)/EDP Science (until 2010), 2016, 73 (1), pp.77- 103. 10.1007/s13595-015-0488-3. hal-01330031 HAL Id: hal-01330031 https://hal.archives-ouvertes.fr/hal-01330031 Submitted on 9 Jun 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Annals of Forest Science (2016) 73:77–103 DOI 10.1007/s13595-015-0488-3 REVIEW PAPER Forest tree genomics: 10 achievements from the past 10 years and future prospects Christophe Plomion1,2 & Catherine Bastien3 & Marie-Béatrice Bogeat-Triboulot4,5 & Laurent Bouffier1,2 & Annabelle Déjardin3 & Sébastien Duplessis6 & Bruno Fady7 & Myriam Heuertz1,2,8 & Anne-Laure Le Gac9 & Grégoire Le Provost1,2 & Valérie Legué 10,11 & Marie-Anne Lelu-Walter3 & Jean-Charles Leplé3 & Stéphane Maury9 & Alexandre Morel3 & Sylvie Oddou-Muratorio7 & Gilles Pilate3 & Léopoldo Sanchez3 & Ivan Scotti7 & Caroline Scotti-Saintagne 7 & Vincent Segura3 & Jean-François Trontin12 & Corinne Vacher1,2 Received: 30 October 2014 /Accepted: 18 May 2015 /Published online: 10 June 2015 # The Author(s) 2015. This article is published with open access at SpringerLink.com Abstract genomics and bioinformatics toolbox has advanced our un- & Key message This review highlights some of the discov- derstanding of the structure, functioning, and evolution of eries and applications made possible by “omics” technol- forest tree genomes. ogies over the last 10 years and provides perspectives for & Aims and methods This review highlights some of the dis- pioneering research to increase our understanding of tree coveries and applications that “omics” technologies have biology. made possible for forest trees over the past 10 years. & Context A decade after the first forest tree genome sequence & Results In this review, we start by our current understanding was released into the public domain, the rapidly evolving of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiot- Handling Editor: Jean-Michel Leban ic stresses. We then skim over advances in interactome anal- ysis and epigenomics, the knowledge of the extent of genetic Contribution of the co-authors CP coordinated this review, defined its variation within and between species, revealing micro- and content, wrote the abstract, introduction, and conclusion sections, and edited the whole manuscript. The following co-authors contributed to the macro-evolutionary processes and species history, together following sections: JCL (2.1), GP (2.2.1), GLP (2.2.2), VL (2.2.3), with the complex architecture of quantitative traits. We finally MALW, AM, and JFT (2.2.4), MBBT (2.3.1), CB and SD (2.3.2), CV end with applications in genetic resource conservation and (2.3.3), AD (2.4), ALLG and SM (2.5), SOM and IS (2.6), MH and CSS breeding. (2.7), VS (2.8), BF (2.9), and LB and LS (2.10). All authors have read and & approved the final manuscript. Conclusion The knowledge gained through the use of these technologies has a huge potential impact for adapting forests Electronic supplementary material The online version of this article (doi:10.1007/s13595-015-0488-3) contains supplementary material, to the main challenges they will have to face: changing de- which is available to authorized users. mand from ecosystem services with potentially conflicting * Christophe Plomion Sébastien Duplessis [email protected] [email protected] Catherine Bastien Bruno Fady [email protected] [email protected] Marie-Béatrice Bogeat-Triboulot Myriam Heuertz [email protected] [email protected] Laurent Bouffier Anne-Laure Le Gac [email protected] [email protected] Annabelle Déjardin Grégoire Le Provost [email protected] [email protected] 78 C. Plomion et al. strategies in terms of conservation and use, as well as climate of sets of genes, right up to complete genomes, with the use of changes and associated threats. Genomics will undoubtedly high-throughput methods. These methods include the struc- play a major role over the next decade and beyond, not only tural characterization of entire genomes, genes, mRNA, and to further understand the mechanisms underlying adaptation proteins, the genome mapping and sequencing (genomics), and evolution but also to develop and implement innovative the study of mRNA, proteins, and metabolite abundances management and policy actions to preserve the adaptability of across different environmental conditions and/or developmen- natural forests and intensively managed plantations. tal stages (functional genomics, i.e., transcriptomics, proteo- mics, metabolomics), the analysis of epigenetic modifications (epigenomics), the inference of evolutionary mechanisms Keywords Genomics .Foresttrees .Developmentalbiology . (comparative and population genomics related to macro- and Epigenetics . Interactome . Micro-evolution . Breeding and micro-evolutionary processes, respectively), and the study of conservation complex biological systems (community genomics, metagenomics). Since the publication of the first tree genome sequence (black cottonwood, Tuskan et al. 2006), technolo- 1 Introduction gies and genetic resources facilitating research into forest tree genomics have advanced our understanding of the tree growth Forest system currently faces a number of major challenges, and development (resulting in large and long-lived organ- including increases in the demand for wood, pressure to con- isms), the responses of trees to intrinsic (ontogenic phase serve forest areas, and global climate change and associated change) and extrinsic (biotic and abiotic) factors, the remark- threats. The adaptation of these systems in response to these able buffering capacity (plasticity) of trees, enabling them to challenges will require a multifaceted approach, in which ge- cope with chronic stresses and extreme events, the molecular nomic sciences have an important role to play. The aim is to basis of genetic variation within and between species, and the apply a series of technologies from the fields of genetics, way in which this variation has been shaped by evolutionary molecular and cell biology fostered by bioinformatics, and forces and its relationship to phenotypic variation and adapta- robotics to analyses of the structure, function, and evolution tion. The objective of this review, which is not intended to be 1 Valérie Legué INRA, UMR1202 BIOGECO, 33612 Cestas, France [email protected] 2 University of Bordeaux, BIOGECO, UMR 1202, Marie-Anne Lelu-Walter 33615 Pessac, France [email protected] 3 INRA, UR0588 AGPF, Amélioration, Génétique et Physiologie Jean-Charles Leplé Forestières, 2163 Avenue de la Pomme de Pin, CS 40001 Ardon, [email protected] 45075 Cedex 2, Orléans, France Stéphane Maury 4 [email protected] INRA, UMR Ecologie et Ecophysiologie Forestière, 25420 Champenoux, France Alexandre Morel 5 [email protected] UMR Ecologie et Ecophysiologie Forestière, Université de Lorraine, BP 239, 54506 Vandoeuvre, France Sylvie Oddou-Muratorio 6 [email protected] INRA, IAM, UMR 1136, 54280 Champenoux, France 7 Gilles Pilate INRA, UR629, URFM, Ecologie des Forêts Méditerranéennes, [email protected] Domaine St Paul, 84914 Avignon, France 8 Léopoldo Sanchez INIA Forest Research Centre, Carretera de A Coruña km 7.5, [email protected] 28040 Madrid, Spain Ivan Scotti 9 [email protected] USC 1328 INRA, Laboratoire de Biologie des Ligneux et des Grandes Cultures, University of Orléans EA 1207, Caroline Scotti-Saintagne 45067 Orléans, France [email protected] Vincent Segura 10 Clermont Université, Université Blaise-Pascal, UMR 547 PIAF, BP [email protected] 10448, 63000 Clermont-Ferrand, France Jean-François Trontin 11 INRA, UMR 547 PIAF, 63100 Clermont-Ferrand, France [email protected] 12 FCBA, Pôle Biotechnologies et Sylviculture avancée, Corinne Vacher 71 route d’Arcachon, 33610 [email protected] Cestas, France Forest tree genomics 79 exhaustive, is to outline the tremendous progress achieved in et al. 2013), together with a second angiosperm tree species, forest tree genomics over the last 10 years. This progress is Eucalyptus (Myburg et al. 2014), and three conifers, Norway illustrated by considering a series of 10 achievements. We will spruce (Nystedt et al. 2013), white spruce (Birol et al. 2013), begin
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