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1. Landscape Agronomy: Lessons Learned and Challenges Ahead, from a European Perspective

Author

Claudine Thenail, Anna-Camilla Moonen, Sylvie Lardon, Elisa Marraccini, Davide Rizzo, Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Center of Plant Sciences, Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP), Territoires (Territoires), AgroParisTech-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Università degli Studi di Udine - University of Udine [Italie], Innovation, Territoire, Agriculture et Agro-industrie, Connaissance et Technologie (INTERACT), UniLaSalle, Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), and Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier

Subjects
Policy-making, Integrated approach, Natural resource management, Farm management, Agriculture, Policy-making, Farm management, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Agriculture, Policymaking, Natural resource management, [SHS.GEO]Humanities and Social Sciences/Geography, Integrated approach
Abstract

International audience; Landscape Agronomy is expected to contribute to the observation, understanding and support of agriculture at the landscape level. The conceptual model of Landscape Agronomy was developed to integrate assessment and monitoring beyond the farm level and across multiple temporal and spatial scales. In this chapter, we evaluate the relevance of the Landscape Agronomy conceptual model by analysing three issues of integrated governance and public action. The three examples highlight the three parts of the conceptual model: (a) core agricultural landscape dynamics, illustrated by farmers’ collective projects of agroecological transition; (b) the three poles of the conceptual model—practices, resources and patterns—illustrated by Integrated Pest Management as an example of requirements for sustainable agroecosystem management; and (c) temporal and spatial interactions, illustrated by the concept of territorial circularity as a way to integrate landscape-based management into global issues related to nutrient cycles. Although it captures the key issues addressed by such perspectives, the Landscape Agronomy conceptual model still faces some challenges, such as explicit consideration of temporal dimensions and explicit inclusion of new (invisible) patterns emerging from newly available data and digitalisation.

Published
2022
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2. Agriculture at the Landscape Level: Scientific Background and Literature Overview

Author

Davide Rizzo, Marta Debolini, Claudine Thenail, Sylvie Lardon, Elisa Marraccini, Innovation, Territoire, Agriculture et Agro-industrie, Connaissance et Technologie (INTERACT), UniLaSalle, Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Division on Impacts on Agriculture, Forests and Ecosystem Services (IAFES), Euro-Mediterranean Center on Climate Change (CMCC), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Territoires (Territoires), AgroParisTech-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), and Università degli Studi di Udine - University of Udine [Italie]

Subjects
Agronomic literature, bibliometric analysis, interdisciplinarity, landscape sciences, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Agronomic literature, conceptual framework, bibliometric analysis, interdisciplinarity, landscape sciences, [SHS.GEO]Humanities and Social Sciences/Geography, conceptual framework
Abstract

International audience; Addressing agriculture at the landscape level leads to dealing with agricultural landscapes, defined here as landscapes that contain mainly agricultural land uses. In this chapter, we focus on how agronomy and other disciplines have addressed to date agriculture beyond field and farm management. The landscape agronomy framework suggests that addressing agriculture at the landscape level allows farmers to be included with other stakeholders involved in spatially explicit management of natural resources. This framework also bridges gaps with other disciplines that work to describe and understand agricultural landscapes and their management. In addition to this qualitative summary of the scientific background, we present results of a bibliometric analysis that used the CorTexT platform to explore research keywords, (inter)disciplinary bridges and emerging issues related to these topics. The results highlighted the emergence of climate change, ecosystem services and management practices in the literature related to agronomic terms, especially when landscape is explicitly mentioned in publications’ titles, abstracts or keywords. In the end, we draw conclusions about potential improvements to this conceptual framework and introduce the structure of the present book about advances and challenges of a territorial approach to agricultural issues.

Published
2022
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3. A quantitative review of on-farm feeding practices to enhance the quality of grassland-based ruminant dairy and meat products

Author

Mauro Coppa, Bernardo Valenti, Valérie Monteils, B. Martin, G. Peratoner, A. Cabiddu, AGRIS sardegna, Research Centre Laimburg, Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Università degli Studi di Udine - University of Udine [Italie], Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Vitamin, Farms, 040301 veterinary sciences, Silage, [SDV]Life Sciences [q-bio], Terpenoids, Vaccenic acid, Forage, Biology, Colour, 0403 veterinary science, chemistry.chemical_compound, Animal science, Ruminant, Animals, Lactation, Fatty acids, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Sheep, Rumenic acid, Animal product, 0402 animal and dairy science, food and beverages, 04 agricultural and veterinary sciences, Ruminants, biology.organism_classification, 040201 dairy & animal science, Animal Feed, Grassland, Carotenoids, Diet, Meat Products, Milk, chemistry, Sensory properties, Animal Science and Zoology, Composition (visual arts), Cattle, Female
Abstract

In the last decades, a large body of evidence has highlighted the major role of feeding management practices in improving specific nutritional, technological and sensory quality traits of ruminant products. However, results have been mostly obtained under controlled conditions, and have been rarely validated on-farm. Therefore, a quantitative review was conducted to quantify the effects of on-farm feeding management practices on carotenoids, fat-soluble vitamins, colour, fatty acids (FAs), terpenes and sensory properties in the main animal product categories (PCs): dairy products from cattle (DC), sheep (DS) and goat (DG), and meat from cattle (MC) and sheep (MS). Four feeding scenarios were selected according to the consistency of on-farm studies in the literature: (a) feeding "Fresh herbage" instead of conserved forages; (b) ban any form of silage ("Silage-free"); (c) ban maize silage ("Maize silage-free"); (d) feeding forages from permanent grasslands rich in species or plant secondary metabolites (PSMs) ("PSM-rich permanent grassland"). Feeding fresh herbage increased the concentration of carotenoids, fat-soluble vitamin, n-3 FA, rumenic acid, and branched chain FA (BCFA), and reduced the concentration of saturated FA, for all PC, with overall stronger effect for dairy products than for meat. The texture of meat and dairy products was marginally affected, whereas feeding fresh herbage decreased lactic and increased vegetal notes in DC. The "Silage-free" feeding scenario resulted in increased vaccenic acid, rumenic acid, BCFA, and C18:3n-3 in DC. The "Maize silage-free" feeding scenario lowered n-6 FA whereas increased n-3, rumenic acid and BCFA concentrations in DC. Feeding ruminants with forages from "PSM-rich permanent grasslands" increased monounsaturated FA, n-3 FA and rumenic acid and decreased n-6 FA in dairy products, and only marginally affected meat FA composition. The DC from "PSM-rich permanent grasslands" showed higher intense, spicy and animal notes. Overall, the differences between feeding management practices observed on farm were smaller than those observed under controlled trials. Several confounding factors, not controlled when operating under on-farm conditions, could be at the origin of these divergences (i.e. mixed diets, forage characteristics, animal-related factors). This review confirmed that farming practices may differently affect several quality traits of ruminant products. It also highlighted the uneven knowledge on the effect of feeding management depending on the PC: larger for milk than for meat and decreasing when moving from cattle to sheep and from sheep to goat.

Published
2022
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4. Cheese quality from cows given a tannin extract in 2 different grazing seasons

Author

M. Caccamo, Giuseppe Luciano, Antonio Natalello, Ruggero Menci, Bernardo Valenti, Mauro Coppa, Teresa Rapisarda, Isabelle Constant, Vincent Niderkorn, Alessandro Priolo, Antonio Difalco, University of Catania [Italy], Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Università degli Studi di Udine - University of Udine [Italie], Consorzio Ricerca Filiera Lattiero Casearia (CORFILAC), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio], Pasture, tannin, 03 medical and health sciences, Rumen, Animal science, Cheese, Genetics, Tannin, Animals, Lactation, Dairy cattle, Dry matter, Cheesemaking, grazing season, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, geography, geography.geographical_feature_category, Chemistry, Plant Extracts, dairy cow, 0402 animal and dairy science, cheese quality, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Animal Feed, Diet, Milk, Food security, food quality and human health, Dietary Supplements, Hay, Animal Science and Zoology, Cattle, Female, Seasons, Tannins, Food Science, Polyunsaturated fatty acid
Abstract

International audience; The aim of the present study was to compare the effect of dietary tannins on cow cheese quality in 2 different grazing seasons in the Mediterranean. Two experiments were performed on 14 dairy cows reared in an extensive system. The first experiment took place in the wet season (WS), and the second experiment took place in the dry season (DS). In the WS and DS experiments, cows freely grazed green pasture or dry stubbles, respectively, and the diet was supplemented with pelleted concentrate and hay. In both experiments, the cows were divided into 2 balanced groups: a control group and a group (TAN) receiving 150 g of tannin extract/head per day. After 23 d of dietary treatment, individual milk was collected, processed into individual cheeses, and aged 25 d. Milk was analyzed for chemical composition, color parameters, and cheesemaking aptitude (laboratory cheese yield and milk coagulation properties). Cheese was analyzed for chemical composition, proteolysis, color parameters, rheological parameters, fatty acid profile, and odor-active volatile compounds. Data from the WS and DS experiments were statistically analyzed separately with an analysis of covariance model. In the WS experiment, dietary tannin supplementation had no effect on milk and cheese parameters except for a reduced concentration of 2-heptanone in cheese. In the DS experiment, TAN milk showed lower urea N, and TAN cheese had lower C18:1 trans-10 concentration and n-6:n-3 polyunsaturated fatty acid ratio compared with the control group. These differences are likely due to the effect of tannins on rumen N metabolism and fatty acid biohydrogenation. Dietary tannins may differently affect the quality of cheese from Mediterranean grazing cows according to the grazing season. Indeed, tannin bioactivity on rumen metabolism seems to be enhanced during the dry season, when diet is low in protein and rich in acid detergent fiber and lignin. The supplementation dose used in this study (1% of estimated dry matter intake) had no detrimental effects on cheese yield or cheesemaking parameters. Also, it is unlikely that sensorial characteristics would be affected by this kind of dietary tannin supplementation.

Published
2021
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5. Ten Years of VINQUEST: First Insight for Breeding New Apple Cultivars With Durable Apple Scab Resistance

Author

Anna Pikunova, Carmen Leida, Pierre-Henri Dubuis, Hilde Nybom, Annemarie Auwerkerken, Thomas Passey, Vincent Philion, Vincent G. M. Bus, Frédérique Didelot, Sylwester Masny, Andreas Spornberger, Danas Baniulis, Hannes Laszakovits, Thomas Rühmer, Franz Ruess, Walter Guerra, Fanny Le Berre, Klaus Strasser, Guido Cipriani, Andreas Wehrli, Klemens Boeck, Stefano Tartarini, Andrea Patocchi, Andreas Peil, Radek Vávra, Martina Staples, Agroscope Changins-Wädeswil, Agroscope, Better3Fruit N.V., Partenaires INRAE, Consorzio Italiano Vivaisti CIV, Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Università degli Studi di Udine - University of Udine [Italie], NIAB EMR, Hohere Bundeslehranstalt & Bundesamt Wein & Obstb, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Inst Rech & Dev Agroenvironm, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Landwirtschaftl Fachschule Eisenstadt, ‎‎ Versuchsstn Obst & Weinbau HaidegG, Landwirtschaftskammer Niedersachsen, Lithuanian Res Ctr Agr & Forestry, Obst Sorten Garten Ohlsdorf, Res & Breeding Inst Pomol, Research Centre Laimburg, Res Inst Hort, Staatliche Lehr & Versuchsanstalt Wein & Obstbau, Station d'expérimentation fruitière La Moriniere, Dept Plant Breeding Balsgard, Swedish University of Agricultural Sciences (SLU), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), University of Vienna [Vienna], All-Russian Research Institute of Fruit Crop Breeding (VNIISPK), and The New Zealand Institute for Plant & Food Research Ltd

Subjects
0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Virulence, Plant Science, Molecular marker, Breeding, Genes, Plant, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Ascomycota, Apple breeding, Apple scab, Durable resistance, Venturia inaequalis, Malus, Plant Diseases, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cultivar, 2. Zero hunger, biology, Resistance (ecology), Plant, biology.organism_classification, Fungal disease, Horticulture, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Genes, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

International audience; Apple scab, caused by Venturia inaequalis, is a major fungal disease worldwide. Cultivation of scab-resistant cultivars would reduce the chemical footprint of apple production. However, new apple cultivars carrying durable resistances should be developed to prevent or at least slow the breakdown of resistance against races of V. inaequalis. One way to achieve durable resistance is to pyramid multiple scab resistance genes in a cultivar. The choice of the resistance genes to be combined in the pyramids should take into account the frequency of resistance breakdown and the geographical distribution of apple scab isolates able to cause such breakdowns. In order to acquire this information and to make it available to apple breeders, the VINQUEST project (www.vinquest.ch) was initiated in 2009. Ten years after launching this project, 24 partners from 14 countries regularly contribute data. From 2009 to 2018 nearly 9000 data points have been collected. This information has been used to identify the most promising apple scab resistance genes for developing cultivars with durable resistance, which to date are: Rvi5, Rvi11, Rvi12, Rvi14 and Rvi15. As expected, Rvi1, together with Rvi3 and Rvi8, were often overcome, hence have little value for scab resistance breeding. Rvi10 may also belong to this group. On the other hand Rvi2, Rvi4, Rvi6, Rvi7, Rvi9, and Rvi13 are still useful for the breeding, but their use is recommended only in extended pyramids of (≥3) resistance genes.

Published
2020
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6. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Author

Thierry Tonon, Jeremy Schmutz, Yao-Cheng Lin, Mats Töpel, Rolf Lohaus, Emanuela Dattolo, Christoffer Boström, Hope Tice, Anna R. Kersting, Jerry Jenkins, Erich Bornberg-Bauer, Pamela J. Green, Jane Grimwood, Florian Maumus, Gabriele Procaccini, Bram Verhelst, Simon M. Dittami, Emanuele De Paoli, Janina Brakel, Mojgan Amirebrahimi, Amy Mraz, Gurvan Michel, Jonas Collén, Mansi Chovatia, Kevin Vanneste, Chiara Lauritano, Alexander Jueterbock, Till Bayer, Pierre Rouzé, Thorsten B. H. Reusch, Gareth A. Pearson, Jeanine L. Olsen, Wytze T. Stam, Yves Van de Peer, Carlos M. Duarte, GELIFES, Ghent University [Belgium] (UGENT), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Napoli, Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Università degli Studi di Udine - University of Udine [Italie], Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Westfälische Wilhelms-Universität Münster (WWU), Heinrich-Heine-Universität Düsseldorf [Düsseldorf], University of Gothenburg (GU), US Department of Energy Joint Genome Institute, University of California, Åbo Akademi University [Turku], HudsonAlpha Institute for Biotechnology, Nord University [Bodø], Amplicon Express Inc., University of Delaware [Newark], University of Algarve [Portugal], King Abdullah University of Science and Technology (KAUST), Christian-Albrechts-Universität zu Kiel (CAU), University of Pretoria [South Africa], Universiteit Gent = Ghent University (UGENT), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], University of California (UC), HudsonAlpha Institute for Biotechnology [Huntsville, AL], and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
0301 basic medicine, Salinity, Acclimatization, PROTEIN, Molecular engineering in plants, Evolutionary ecology, Plant evolution, Osmoregulation, Adaptation, Physiological, Cell Wall, Ethylenes, Gene Duplication, Genes, Plant, Genome, Plant, Metabolic Networks and Pathways, Molecular Sequence Data, Oceans and Seas, Phylogeny, Plant Leaves, Plant Stomata, Pollen, Salt-Tolerance, Seaweed, Terpenes, Zosteraceae, Evolution, Molecular, Seawater, Medicine (all), Multidisciplinary, ECOSYSTEMS, RNA-SEQ, MAXIMUM-LIKELIHOOD, NEW-JERSEY, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Genome, Ecology, FLOWERING PLANTS, food and beverages, Salt Tolerance, Seagrass, Mathematics and natural science: 400::Zoology and botany: 480::Marine biology: 497 [VDP], Zostera marina, CHROMOSOME-NUMBERS, Evolution, General Science & Technology, Physiological, Biology, 03 medical and health sciences, GENE LISTS, Botany, Genetics, Ecosystem, Marine ecosystem, 14. Life underwater, Genetic variation, Adaptation, Life Below Water, SEQUENCES, Human Genome, fungi, Biology and Life Sciences, Molecular, Plant, biology.organism_classification, Zostera marina Linnaeus, 1758, 030104 developmental biology, Genes
Abstract

Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.

Published
2016
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7. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance

Author

Véronique de Berardinis, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Raffaella Marconi, Sophie Paillard, Gabriele Di Gaspero, Anne-Françoise Adam-Blondon, Cécile Guichard, Isabelle Le Clainche, Legeai Fabrice, Raffaele Testolin, Véronique Brunaud, Corinne Cruaud, Michele Morgante, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Agrarie e Ambientali (DiSA), Università degli Studi di Udine - University of Udine [Italie], Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Dipartimento di Matematica e Informatica - Universita Udine (DIMI), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Candidate gene, carte génétique, système immunitaire, Sequence assembly, Plant Science, 01 natural sciences, Genome, Polymerase Chain Reaction, maladie fongique, lcsh:Botany, RICE GENOME, Vitis, PLANT IMMUNE SYSTEM, 2. Zero hunger, Genetics, 0303 health sciences, Vegetal Biology, Contig, NONHOST RESISTANCE, Physical Chromosome Mapping, GENOME SEQUENCE, food and beverages, ARABIDOPSIS, lcsh:QK1-989, mildiou, gène candidat, Genome, Plant, Research Article, Signal Transduction, résistance aux maladies, Heterozygote, GENETICS, Biology, Genes, Plant, DNA sequencing, Chromosomes, Plant, LINKAGE MAP, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genome size, 030304 developmental biology, Plant Diseases, BAC, Whole genome sequencing, VITIS VINIFERA L, POWDERY MILDEW, GENETIQUE, cabernet sauvignon, Sequence Analysis, DNA, séquence nucléotidique, Immunity, Innate, cartographie, vigne, Biologie végétale, 010606 plant biology & botany
Abstract

Background Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. Results The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. Conclusion Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.

Published
2008
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8. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

Author

Graziano Pesole, Benjamin Noel, François Artiguenave, Alberto Policriti, Federica Cattonaro, Alessandro Vezzi, Delphine Jublot, Valérie Laucou, Michel Gouyvenoux, Eléonore Durand, Didier Merdinoglu, Cristian Del Fabbro, Giorgio Valle, Isabelle Le Clainche, Michael Alaux, Irena Juman, Erica Mica, Béatrice Segurens, Alberto Casagrande, Claude Scarpelli, Massimo Delledonne, Gabriele Di Gaspero, Jean-Marc Aury, David S. Horner, Marco Moroldo, M. Enrico Pè, Philippe Hugueney, Mario Pezzotti, Michel Caboche, Anne-Françoise Adam-Blondon, Véronique Anthouard, Nicola Vitulo, Alain Lecharny, Alain Billault, Virginie Vico, Olivier Jaillon, Christian Clepet, Sébastien Aubourg, Michele Morgante, Jean Weissenbach, Patrick Wincker, Nathalie Choisne, Aurélie Canaguier, Corinne Dasilva, Edgardo Ugarte, Philippe Chatelet, Clémence Bruyère, Vincent Dumas, Sophie Paillard, Fabrice Legeai, Nicoletta Felice, Simone Scalabrin, G Malacrida, Julie Poulain, Francis Quetier, Claire Jubin, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Dipartimento di Matematica e Informatica - Universita Udine (DIMI), Università degli Studi di Udine - University of Udine [Italie], Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), CRIBI (CRIBI), Università degli Studi di Padova = University of Padua (Unipd), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano = University of Milan (UNIMI), Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Istituto Tecnologie Biomediche, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Dipartimento Scientifico e Tecnologico (DST), Università degli studi di Verona = University of Verona (UNIVR), Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, VIGNA-CRA Initiative (VIGNA-CRA INITIATIVE), Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Universita degli Studi di Padova, Università degli Studi di Milano [Milano] (UNIMI), Università degli studi di Bari Aldo Moro (UNIBA), Consiglio Nazionale delle Ricerche [Roma] (CNR), University of Verona (UNIVR), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Università degli studi di Milano [Milano], Università degli studi di Bari, Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Università degli Studi di Verona, O., Jaillon, J., Aury, B., Noel, A., Policriti, C., Clepet, Casagrande, Alberto, N., Choisne, S., Aubourg, N., Vitulo, C., Jubin, A., Vezzi, F., Legeai, P., Hugueney, C., Dasilva, D., Horner, E., Mica, D., Jublot, J., Poulain, C., Bruyère, A., Billault, B., Seguren, M., Gouyvenoux, E., Ugarte, F., Cattonaro, V., Anthouard, V., Vico, C., DEL FABBRO, M., Alaux, G., DI GASPERO, V., Duma, N., Felice, S., Paillard, I., Juman, M., Moroldo, S., Scalabrin, A., Canaguier, I., LE CLAINCHE, G., Malacrida, E., Durand, G., Pesole, V., Laucou, P., Chatelet, D., Merdinoglu, M., Delledonne, M., Pezzotti, A., Lecharny, C., Scarpelli, F., Artiguenave, M. E., Pè, G., Valle, M., Morgante, M., Caboche, A., ADAM BLONDON, J., Weissenbach, F., Quétier, and P., Wincker

Subjects
0106 biological sciences, genotype, Arabidopsis, POLYPLOIDY, adaptation, 01 natural sciences, Genome, RNA, Transfer, Gene duplication, plant genomics, plant genome evolution, Sequencing, Vitis, vitis vinifera, genome sequencing, 2. Zero hunger, Genetics, Plant evolution, 0303 health sciences, Multidisciplinary, food and beverages, Exons, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Paleopolyploidy, Populus, RNA, Plant, ARABIDOPSIS-THALIANA, DNA-SEQUENCE, GENE, DUPLICATION, MAP, IDENTIFICATION, EVOLUTION, DNA, Intergenic, vine, Genome, Plant, assembly, Bioinformatics, Molecular Sequence Data, Genomics, Biology, Genes, Plant, Monocotyledon, DNA sequencing, Evolution, Molecular, Polyploidy, 03 medical and health sciences, evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, angiosperm, genome, 030304 developmental biology, Whole genome sequencing, fungi, Oryza, Sequence Analysis, DNA, 15. Life on land, chronology, Introns, grapevine, MicroRNAs, polyploidy, Karyotyping, vitis classification, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract

International audience; The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

Published
2007
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