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1. Accounting for competition in multi-environment tree genetic evaluations: a case study with hybrid pines

Author

Nuno Borralho, Eduardo P. Cappa, Ector Belaber, Maria Elena Gauchat, Cristian Damián Schoffen, Facundo Muñoz, Leopoldo Sanchez, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), RAIZ – Forestry & Paper Research Institut, Instituto Superior Técnico, Universidade Técnica de Lisboa, Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and This study was funded by the National Institute of Agricultural Technology (INTA) (grant numbers PNFOR-01104062, MSNES-1242204/5). E.P.C.’s research was partially supported by the National Agency for the Promotion of Science and Technology of Argentina (ANPCYT, PICT-2016 1048). F.M.’s research is partially supported by research grant MTM2016-77501-P from the State Research Agency of the Spanish Ministry of Science, Innovation and Universities jointly with the European Regional Development Fund, FEDER.

Subjects
Additive and competition genotype–environment interaction, 0106 biological sciences, Mixed model, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Accounting, Tree breeding, 010603 evolutionary biology, 01 natural sciences, Genetic correlation, Competition (biology), Competition model, Genetic variation, Gene–environment interaction, media_common, Mathematics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, business.industry, Diameter at breast height, Forestry, 15. Life on land, Total heritable variance, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany
Abstract

International audience; Key message: A novel multi-environment competition individual-tree mixed model resulted in better fit, and greater individual narrow- and broad-sense heritabilities than the model without competition, notably for traits showing competition. In multi-environment tests, the proposed model would allow tree breeders to select genotypes with the best performance in both additive direct and competition breeding values, increasing forest productivity. Context: Genetic merit of trees is known to be affected and interact with local competition effects as well as changes across environmental conditions. Recent studies showed that competition genetic effects can affect the genetic variance and bias the tree breeding values, and its covariance with direct breeding values has been variable across traits. Aims: The present paper extends a mixed-model methodology to the problem of accounting for competition in a multi-environment set of forest genetic trials and exploring its impact on genetic variances as well as the multi-environment genetic correlation. Methods: The proposed model is illustrated using data from two full-sib trials of Pinus elliottii var. elliottii × Pinus caribaea var. hondurensis F1. Dispersion parameters and (co)variance of total breeding values were estimated for diameter at breast height, total tree height, and stem straightness at age 10. Results: For traits showing competition effects (diameter at breast height and total tree height), the proposed multi-environment competition model gave better fit than the simpler model. Accounting for competition increased the direct additive variance, reduced the residual variances, and did not change significantly the across-site additive genetic correlation. However, for diameter at breast height, top 5% best genetic rankings showed differences. Conclusion: When traits are strongly affected by inter-tree competition, the use of the proposed model in multi-environment analyses can efficiently identify the phenomenon with general benefits in the fitting of genetic components and open the door to select on the basis of competitiveness.

Published
2021

2. Long cold exposure induces transcriptional and biochemical remodelling of xylem secondary cell wall in Eucalyptus

Author

Victor Carocha, Raphael Ployet, Jacqueline Grima-Pettenati, Marçal Soler, Nathalie Ladouce, Ana Alves, Luc Harvengt, José-Carlos Rodrigues, Christiane Marque, Chantal Teulières, Fabien Mounet, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), RAIZ – Forestry & Paper Research Institut, Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Centro de Estudos Florestais, Technical University of Lisbon-Instituto Superior de Agronomia, Laboratoire de Biotechnologie, Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and FCBA

Subjects
0106 biological sciences, 0301 basic medicine, Physiology, Plant Science, Biology, 01 natural sciences, Cell wall, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Cell Wall, Gene Expression Regulation, Plant, Xylem, Botany, Lignin, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, Hybrid, Regulation of gene expression, Eucalyptus, Abiotic stress, Gene Expression Profiling, food and beverages, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], 15. Life on land, Cold Temperature, 030104 developmental biology, chemistry, Secondary cell wall, 010606 plant biology & botany
Abstract

Although eucalypts are the most planted hardwood trees worldwide, the majority of them are frost sensitive. The recent creation of frost-tolerant hybrids such as Eucalyptus gundal plants (E. gunnii × E. dalrympleana hybrids), now enables the development of industrial plantations in northern countries. Our objective was to evaluate the impact of cold on the wood structure and composition of these hybrids, and on the biosynthetic and regulatory processes controlling their secondary cell-wall (SCW) formation. We used an integrated approach combining histology, biochemical characterization and transcriptomic profiling as well as gene co-expression analyses to investigate xylem tissues from Eucalyptus hybrids exposed to cold conditions. Chilling temperatures triggered the deposition of thicker and more lignified xylem cell walls as well as regulation at the transcriptional level of SCW genes. Most genes involved in lignin biosynthesis, except those specifically dedicated to syringyl unit biosynthesis, were up-regulated. The construction of a co-expression network enabled the identification of both known and potential new SCW transcription factors, induced by cold stress. These regulators at the crossroads between cold signalling and SCW formation are promising candidates for functional studies since they may contribute to the tolerance of E. gunnii × E. dalrympleana hybrids to cold.

Published
2018

3. The genome of Eucalyptus grandis

Author

Anand Raj Kumar Kullan, Erich Bornberg-Bauer, Christopher M. Sullivan, Florent Murat, Elisson Romanel, Yves Van de Peer, Aaron Liston, Priya Ranjan, Dorothy A. Steane, Justin Elser, Pooja Singh, Victor Carocha, Orzenil B. Silva-Junior, Marçal Soler, Cesar Petroli, Inna Dubchak, Jane Grimwood, Carsten Külheim, Danielle A. Faria, Ida Van Jaarsveld, Chu-Yu Ye, Giancarlo Pasquali, Charles A. Hefer, Desre Pinard, Roberto C. Togawa, Richard D. Hayes, Eshchar Mizrachi, Fourie Joubert, Erika Lindquist, Kevin Vanneste, Philippe Rigault, Jérôme Salse, Karen Van der Merwe, David Kudrna, Palitha Dharmwardhana, Gerald A. Tuskan, Diane Bauer, Alexandre Poliakov, Marcio Alves-Ferreira, Kerrie Barry, Vindhya Amarasinghe, Ting Li, William J. Foley, Georgios J. Pappas, Carolina Sansaloni, René E. Vaillancourt, Marília de Castro Rodrigues Pappas, Uffe Hellsten, Daniel S. Rokhsar, Martin Ranik, Anna R. Kersting, Alexander Andrew Myburg, Hua Cassan-Wang, David Goodstein, Christophe Dunand, Naijib Saidi, Timothy J. Tschaplinski, Sushma Naithani, Dario Grattapaglia, Pankaj Jaiswal, Steven G. Hussey, Jeremy Schmutz, Rajani Raja, Brad M. Potts, Margaret Byrne, Antanas V. Spokevicius, Jorge A. P. Paiva, Jacqueline Grima-Pettenati, Xiaohan Yang, Alexander Boyd, Hope Tice, Joseph W. Spatafora, Lieven Sterck, Jerry Jenkins, Steven H. Strauss, Sérgio Hermínio Brommonschenkel, Josquin Tibbits, Rebecca C. Jones, Kelly J. Vining, Hélène San Clemente, BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, DOE Joint Genome Institute [Walnut Creek], Department of Epidemiology & Population Health, London School of Hygiene and Tropical Medicine (LSHTM), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, US Department of Energy Joint Genome Institute, University of California, Embrapa Uva e Vinho (BRAZIL), Technicolor R & I [Cesson Sévigné], Technicolor, Department of Plant Systems Biology, State University of Ghent, Ghent University [Belgium] (UGENT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), Department of Botany and Plant Pathology, Oregon State University (OSU), RAIZ – Forestry & Paper Research Institut, Laboratory of Plant Cell Biotechnology, ITQB/IBET, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, GYDLE, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences-University of Pretoria [South Africa], Institute of Continuing Medical Education of Ioannina, Plastes et différenciation cellulaire (PDC), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Dynamique et Evolution des Parois cellulaires végétales, Office of Science of the US Department of Energy [DE-AC02-05CH11231], Office of Biological and Environmental Research in the US Department of Energy Office of Science, US DOE Bioenergy Center [DE-AC05-00OR22725], Brazilian Ministry of Science, Technology and Innovation (MCTI) through (CNPq), Brazilian Ministry of Science, Technology and Innovation (MCTI) through (FINEP), Brazilian Federal District Research Foundation (FAP-DF), Technology and Human Resources for Industry Programme (THRIP) [UID 80118], South African Department of Science and Technology (DST), National Research Foundation (NRF) [UID 18312, 86936], Laboratoire d'Excellence [LABEX TULIP ANR-10-LABX-41], Agence Nationale pour la Recherche (Project Tree For Joules) [ANR-2010-KBBE-007-01], Fundacao para a Ciencia e Tecnologia (FCT) [P-KBBE/AGR_GPL/0001/2010], Centre National pour la Recherche Scientifique (CNRS), University Paul Sabatier Toulouse III (UPS), Ghent University, Hercules Foundation, Flemish Government-department EWI, Myburg, Alexander A., University of California (UC), Universiteit Gent = Ghent University (UGENT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)

Subjects
Genome evolution, DATABASE, phylogénomique, [SDV]Life Sciences [q-bio], Biology, Genome, DNA sequencing, Evolution, Molecular, Phylogenomics, Myrtales, Botany, Inbreeding depression, TOOL, Inbreeding, RNA-SEQ, PLANT, NUCLEAR-DNA, Phylogeny, ComputingMilieux_MISCELLANEOUS, Eucalyptus, Multidisciplinary, FOREST TREES, Biology and Life Sciences, Genetic Variation, métabolisme secondaire, 15. Life on land, biology.organism_classification, GENE, EVOLUTION, ALIGNMENT, biocarburant, Biofuels, Eucalyptus globulus, évolution du génome, WHOLE-GENOME, Secondary metabolism, Genome, Plant
Abstract

International audience; Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

Published
2014

4. Transcript profiling of Eucalyptus xylem genes during tension wood formation

Author

Pierre Sivadon, António Mendes de Sousa, Victor Carocha, Cristina Marques, Etienne Paux, Jacqueline Grima-Pettenati, Nuno Borralho, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), RAIZ – Forestry & Paper Research Institut, Instituto de Investigação da Floresta e Papel, Partenaires INRAE, Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Régulation et Dynamique de la Formation du Bois, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut pluridisciplinaire de recherche sur l'environnement et les matériaux (IPREM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Physiology, [SDV]Life Sciences [q-bio], Plant Science, Biology, xylem, 01 natural sciences, Transcriptome, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, transcript profiling, Botany, Gene expression, Lignin, RNA, Messenger, Gene, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Eucalyptus, Gene Expression Profiling, Xylem, Gene Expression Regulation, Developmental, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 15. Life on land, Wood, Biomechanical Phenomena, chemistry, RNA, Plant, tension wood formation, Secondary cell wall, secondary cell wall, cDNA array, 010606 plant biology & botany, Gravitation, clustering
Abstract

International audience; Tension wood formed in response to gravitational force is a striking example of the plasticity of angiosperm wood. In this study our goal was to characterize the early changes in gene expression during tension wood formation in Eucalyptus.Using cDNA array technology, transcript profiling of 231 genes preferentially expressed in differentiating Eucalyptus xylem was followed from 6 h to 1 wk of a tension time course of artificially bent Eucalyptus trees.196 genes were differentially regulated between control and bent trees, some exhibiting distinctive expression patterns related to changes in secondary cell wall structure and composition. For instance, expression of a cellulose synthase gene was well correlated with the appearance of the G-layers. Cluster correlation analysis revealed differential regulation of lignin biosynthetic genes and may also be used to help infer the function of unknown gene products.Eucalyptus wood transcriptome analysis during tension wood formation not only provided new clues into the transcriptional regulatory network of genes preferentially expressed in xylem, but also highlighted candidate genes responsible for the genetic and environmentally induced variation of wood quality traits.

Published
2005

5. Xylanase treatment of eucalypt kraft pulps: effect of carryover.

Author

Matos JMS, Evtuguin DV, de Sousa APM, and Carvalho MGVS

Subjects
Oxygen chemistry, Paper
Abstract

The influence of pulp carryover on the efficiency of the xylanase (X) treatment of industrial unbleached and oxygen-delignified eucalypt kraft pulps (A1 and A2 pulps, with kappa number (KN) values of 16 and 10, respectively), collected at the same pulp mill, was studied regarding the consumption of bleaching chemicals and pulp bleachability. Another non-oxygen-delignified eucalyptus kraft pulp of KN 13 was received after the extended cooking from a different pulp mill (pulp B). The assays were performed with both lab-washed (carryover-free) and unwashed (carryover-rich) pulps. Both lab-washed and unwashed pulps with carryover were subjected to X treatment, the former being demonstrating considerably higher ClO 2 savings than the pulps containing carryover. The savings of bleaching reagents were higher when the X stage was applied to the A1 pulp than to the A2 pulp. This advantage of A1 pulp, however, was not confirmed when using unwashed pulps. In contrast, the gains obtained from the X treatment of unwashed pulp A2 were practically as high as those observed for the lab-washed A2 pulp. Furthermore, a similar effect in X stage was recorded for unwashed pulps having close KN: oxygen-delignified A2 pulp and non-oxygen-delignified B pulp. The results suggest that pulp carryover and initial pH were the key factors relating to the effectiveness of X treatment. The application of X treatment to the A2 unwashed pulp (after the oxygen stage) not only saved 20% of the ClO 2 and 10% of the sodium hydroxide, but also improved the brightness stability of the bleached pulp without affecting its papermaking properties. KEY POINTS: • Xylanase treatment boosts kraft pulp bleaching • Pulp carryover hinders the xylanase treatment • Nearly 20% of ClO2 and 10% NaOH savings can be reached using xylanase., (© 2024. The Author(s).)

Published
2024
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6. Effect of enzymatic treatment on Eucalyptus globulus vessels passivation.

Author

Vaz Á, Coelho J, Costa V, Maloney T, Phiri J, Pinto P, de Sousa AM, and Simões R

Subjects
Carbohydrates, Industry, Chlorine, Paper, Eucalyptus chemistry, Cellulases
Abstract

Hardwood vessel elements generate problems in industrial uncoated wood-free printing paper operation, causing vessel picking and ink refusal. These problems are mitigated using mechanical refining at the cost of paper quality. Vessel enzymatic passivation, altering its adhesion to the fiber network and reducing its hydrophobicity is a way of improving paper quality. The object of this paper is to study how the enzymatic treatment by xylanase and by an enzymatic cocktail containing cellulases and laccases affect elemental chlorine free bleached Eucalyptus globulus vessel and fiber porosities, bulk, and surface chemical compositions. Thermoporosimetry revealed the vessel structure to be more porous, surface analysis showed its lower O/C ratio and bulk chemistry analysis its higher hemicellulose content. Enzymes had different effects on porosity, bulk and surface composition of fibers and vessels, affecting vessel adhesion and hydrophobicity. Vessel picking count decreased 76% for papers containing vessels treated with xylanase and 94% for the papers with vessels treated with the enzymatic cocktail. Fiber sheet samples had lower water contact angle (54.1º) than vessels rich sheets (63.7º), that reduced with xylanase (62.1º) and cocktail (58.4º). It is proposed that differences in vessel and fiber porosity structures affect the enzymatic attacks, eventually causing vessel passivation., (© 2023. The Author(s).)

Published
2023
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