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1. End-to-end multimodal 3D imaging and machine learning workflow for non-destructive phenotyping of grapevine trunk internal structure

Author

Romain Fernandez, Loïc Le Cunff, Samuel Mérigeaud, Jean-Luc Verdeil, Julie Perry, Philippe Larignon, Anne-Sophie Spilmont, Philippe Chatelet, Maïda Cardoso, Christophe Goze-Bac, and Cédric Moisy

Subjects
3D imaging, Image processing, MRI, X-ray CT, Plant phenotyping, Plant diseases, Medicine, Science
Abstract

Abstract Quantifying healthy and degraded inner tissues in plants is of great interest in agronomy, for example, to assess plant health and quality and monitor physiological traits or diseases. However, detecting functional and degraded plant tissues in-vivo without harming the plant is extremely challenging. New solutions are needed in ligneous and perennial species, for which the sustainability of plantations is crucial. To tackle this challenge, we developed a novel approach based on multimodal 3D imaging and artificial intelligence-based image processing that allowed a non-destructive diagnosis of inner tissues in living plants. The method was successfully applied to the grapevine (Vitis vinifera L.). Vineyard’s sustainability is threatened by trunk diseases, while the sanitary status of vines cannot be ascertained without injuring the plants. By combining MRI and X-ray CT 3D imaging with an automatic voxel classification, we could discriminate intact, degraded, and white rot tissues with a mean global accuracy of over 91%. Each imaging modality contribution to tissue detection was evaluated, and we identified quantitative structural and physiological markers characterizing wood degradation steps. The combined study of inner tissue distribution versus external foliar symptom history demonstrated that white rot and intact tissue contents are key-measurements in evaluating vines’ sanitary status. We finally proposed a model for an accurate trunk disease diagnosis in grapevine. This work opens new routes for precision agriculture and in-situ monitoring of tissue quality and plant health across plant species.

Published
2024
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2. A Review on Potential Mechanically Resistant Materials for Optical Multifunctional Surfaces: Bioinspired Surfaces with Advanced Properties

Author

Rim Sarieddine, Hind Kadiri, Bruno Guelorget, Loïc Le Cunff, Akram Alhussein, Roland Habchi, and Gilles Lérondel

Subjects
anti‐reflective coatings, biomimetic, hard materials, harsh environments, mechanical resistance, multifunctional surfaces, Physics, QC1-999, Technology
Abstract

Abstract Mimicking naturethrough nanostructuring allows the creation of multifunctional surfaces withremarkable properties, such as anti‐reflectivity, high optical transmittanceand controlled wettability, enabling anti‐icing or anti‐fogging behaviors. These multifunctionalsurfaces have gained significant interest in civil and military domains. However,integrating them into real‐life applications faces challenges related tocost, high‐throughput large‐scale compatible nanofabrication techniques, andtheir mechanical resistance. While sub‐wavelength patterning improves the optical performance,it often comes at the cost of compromising the mechanical resistance. As opticalperformance improves, mechanical resistance tends to deteriorate, and viceversa. To address this challenge, taking inspiration from the lotus leafstructure, where patterns are covered by a thin 2D wax film, covering thepatterns of structured surfaces with a protective layer can be a viablesolution. This protective layer should enhance the mechanical resistance of thesurface without compromising its multifunctional capabilities. This reviewhighlights the most suitable materials that can be employed as protectivecoatings and their potential to enhance the resistance of structured surfaces.The fundamental concept behind the creation of multifunctional optical surfacesis discussed, followed by a comprehensive examination of mechanical tests thatcan be utilized to characterize their mechanical behavior. This review aims topave the way for the development of durable multifunctional optical surfaces,making them more amenable to industrial applications.

Published
2024
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3. Interest of phenomic prediction as an alternative to genomic prediction in grapevine

Author

Charlotte Brault, Juliette Lazerges, Agnès Doligez, Miguel Thomas, Martin Ecarnot, Pierre Roumet, Yves Bertrand, Gilles Berger, Thierry Pons, Pierre François, Loïc Le Cunff, Patrice This, and Vincent Segura

Subjects
Phenomic prediction, Genomic prediction, Plant breeding, Spectroscopy, Phenomics, Grapevine, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

Abstract Background Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum provides information on the biochemical composition within a tissue, itself being under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been mainly applied in several annual crop species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits, related to berry composition, phenology, morphological and vigour. A major novelty of this study was to collect spectra and phenotypes several years apart from each other. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. Results For the first time, we showed that the similarity between spectra and genomic relationship matrices was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Applying a mixed model on spectra data increased phenomic predictive ability, while using spectra collected on wood or leaves from one year or another had less impact. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, a significant positive correlation was found across traits between predictive ability of genomic and phenomic predictions. Conclusion NIRS is a new low-cost alternative to genotyping for predicting complex traits in perennial species such as grapevine. Having spectra and phenotypes from different years allowed us to exclude genotype-by-environment interactions and confirms that phenomic prediction can rely only on genetics.

Published
2022
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4. Characterization of genetic determinants of the resistance to phylloxera, Daktulosphaira vitifoliae, and the dagger nematode Xiphinema index from muscadine background

Author

Bernadette Rubio, Guillaume Lalanne-Tisné, Roger Voisin, Jean-Pascal Tandonnet, Ulysse Portier, Cyril Van Ghelder, Maria Lafargue, Jean-Pierre Petit, Martine Donnart, Benjamin Joubard, Pierre-François Bert, Daciana Papura, Loïc Le Cunff, Nathalie Ollat, and Daniel Esmenjaud

Subjects
Grapevine, Rootstock, Phylloxera, Nematode, Genetic architecture, Pest resistance, Botany, QK1-989
Abstract

Abstract Background Muscadine (Muscadinia rotundifolia) is known as a resistance source to many pests and diseases in grapevine. The genetics of its resistance to two major grapevine pests, the phylloxera D. vitifoliae and the dagger nematode X. index, vector of the Grapevine fanleaf virus (GFLV), was investigated in a backcross progeny between the F1 resistant hybrid material VRH8771 (Vitis-Muscadinia) derived from the muscadine R source ‘NC184–4’ and V. vinifera cv. ‘Cabernet-Sauvignon’ (CS). Results In this pseudo-testcross, parental maps were constructed using simple-sequence repeats markers and single nucleotide polymorphism markers from a GBS approach. For the VRH8771 map, 2271 SNP and 135 SSR markers were assembled, resulting in 19 linkage groups (LG) and an average distance between markers of 0.98 cM. Phylloxera resistance was assessed by monitoring root nodosity number in an in planta experiment and larval development in a root in vitro assay. Nematode resistance was studied using 10–12 month long tests for the selection of durable resistance and rating criteria based on nematode reproduction factor and gall index. A major QTL for phylloxera larval development, explaining more than 70% of the total variance and co-localizing with a QTL for nodosity number, was identified on LG 7 and designated RDV6. Additional QTLs were detected on LG 3 (RDV7) and LG 10 (RDV8), depending on the in planta or in vitro experiments, suggesting that various loci may influence or modulate nodosity formation and larval development. Using a Bulked Segregant Analysis approach and a proportion test, markers clustered in three regions on LG 9, LG 10 and LG 18 were shown to be associated to the nematode resistant phenotype. QTL analysis confirmed the results and QTLs were thus designated respectively XiR2, XiR3 and XiR4, although a LOD-score below the significant threshold value was obtained for the QTL on LG 18. Conclusions Based on a high-resolution linkage map and a segregating grapevine backcross progeny, the first QTLs for resistance to D. vitifoliae and to X. index were identified from a muscadine source. All together these results open the way to the development of marker-assisted selection in grapevine rootstock breeding programs based on muscadine derived resistance to phylloxera and to X. index in order to delay GFLV transmission.

Published
2020
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5. Cultivar Diversity of Grape Skin Polyphenol Composition and Changes in Response to Drought Investigated by LC-MS Based Metabolomics

Author

Lucie Pinasseau, Anna Vallverdú-Queralt, Arnaud Verbaere, Maryline Roques, Emmanuelle Meudec, Loïc Le Cunff, Jean-Pierre Péros, Agnès Ageorges, Nicolas Sommerer, Jean-Claude Boulet, Nancy Terrier, and Véronique Cheynier

Subjects
grape berry, Vitis vinifera, phenolic compounds, UHPLC-QqQ-MS, metabolomics, water deficit, Plant culture, SB1-1110
Abstract

Phenolic compounds represent a large family of plant secondary metabolites, essential for the quality of grape and wine and playing a major role in plant defense against biotic and abiotic stresses. Phenolic composition is genetically driven and greatly affected by environmental factors, including water stress. A major challenge for breeding of grapevine cultivars adapted to climate change and with high potential for wine-making is to dissect the complex plant metabolic response involved in adaptation mechanisms. A targeted metabolomics approach based on ultra high-performance liquid chromatography coupled to triple quadrupole mass spectrometry (UHPLC-QqQ-MS) analysis in the Multiple Reaction Monitoring (MRM) mode has been developed for high throughput profiling of the phenolic composition of grape skins. This method enables rapid, selective, and sensitive quantification of 96 phenolic compounds (anthocyanins, phenolic acids, stilbenoids, flavonols, dihydroflavonols, flavan-3-ol monomers, and oligomers…), and of the constitutive units of proanthocyanidins (i.e., condensed tannins), giving access to detailed polyphenol composition. It was applied on the skins of mature grape berries from a core-collection of 279 Vitis vinifera cultivars grown with or without watering to assess the genetic variation for polyphenol composition and its modulation by irrigation, in two successive vintages (2014–2015). Distribution of berry weights and δ13C values showed that non irrigated vines were subjected to a marked water stress in 2014 and to a very limited one in 2015. Metabolomics analysis of the polyphenol composition and chemometrics analysis of this data demonstrated an influence of water stress on the biosynthesis of different polyphenol classes and cultivar differences in metabolic response to water deficit. Correlation networks gave insight on the relationships between the different polyphenol metabolites and related biosynthetic pathways. They also established patterns of polyphenol response to drought, with different molecular families affected either positively or negatively in the different cultivars, with potential impact on grape and wine quality.

Published
2017
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6. Comparative transcriptome of wild type and selected strains of the microalgae Tisochrysis lutea provides insights into the genetic basis, lipid metabolism and the life cycle.

Author

Gregory Carrier, Matthieu Garnier, Loïc Le Cunff, Gaël Bougaran, Ian Probert, Colomban De Vargas, Erwan Corre, Jean-Paul Cadoret, and Bruno Saint-Jean

Subjects
Medicine, Science
Abstract

The applied exploitation of microalgae cultures has to date almost exclusively involved the use of wild type strains, deposited over decades in dedicated culture collections. Concomitantly, the concept of improving algae with selection programs for particular specific purposes is slowly emerging. Studying since a decade an economically and ecologically important haptophyte Tisochrysis lutea (Tiso), we took advantage of the availability of wild type (Tiso-Wt) and selected (Tiso-S2M2) strains to conduct a molecular variations study. This endeavour presented substantial challenges: the genome assembly was not yet available, the life cycle unknown and genetic diversity of Tiso-Wt poorly documented. This study brings the first molecular data in order to set up a selection strategy for that microalgae. Following high-throughput Illumina sequencing, transcriptomes of Tiso-Wt and Tiso-S2M2 were de novo assembled and annotated. Genetic diversity between both strains was analyzed and revealed a clear conservation, while a comparison of transcriptomes allowed identification of polymorphisms resulting from the selection program. Of 34,374 transcripts, 291 were differentially expressed and 165 contained positional polymorphisms (SNP, Indel). We focused on lipid over-accumulation of the Tiso-S2M2 strain and 8 candidate genes were identified by combining analysis of positional polymorphism, differential expression levels, selection signature and by study of putative gene function. Moreover, genetic analysis also suggests the existence of a sexual cycle and genetic recombination in Tisochrysis lutea.

Published
2014
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7. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L.

Author

Grégory Carrier, Loïc Le Cunff, Alexis Dereeper, Delphine Legrand, François Sabot, Olivier Bouchez, Laurent Audeguin, Jean-Michel Boursiquot, and Patrice This

Subjects
Medicine, Science
Abstract

Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.

Published
2012
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8. Beyond the foliage: Using non-destructive multimodal 3D imaging and AI to phenotype and diagnose trunk diseases

Author

Romain Fernandez, Loïc Le Cunff, Samuel Mérigeaud, Jean-Luc Verdeil, Julie Perry, Philippe Larignon, Anne-Sophie Spilmont, Philippe Chatelet, Maïda Cardoso, Christophe Goze-Bac, and Cédric Moisy

Abstract

Quantifying healthy and degraded inner tissues in plants is of great interest in agronomy, for example, to assess plant health and quality and monitor physiological traits or diseases. However, detecting functional and degraded plant tissuesin-vivowithout harming the plant is extremely challenging. New solutions are needed in ligneous and perennial species, for which the sustainability of plantations is crucial. To tackle this challenge, we developed a novel approach based on multimodal 3D imaging and Artificial Intelligence (AI)-based image processing that allowed a noninvasive diagnosis of inner tissues in living plants. The method was successfully applied to the grapevine (Vitis viniferaL.) in vineyards where sustainability was threatened by trunk diseases, while the sanitary status of vines cannot be ascertained without injuring the plants. By combining MRI and X-ray CT 3D imaging with an automatic voxel classification, we could discriminate intact, degraded, and white rot tissues with a mean global accuracy of over 91%. Each imaging modality contribution to tissue detection was evaluated, and we identified quantitative structural and physiological markers characterizing wood degradation steps. The combined study of inner tissue distributionversusexternal foliar symptom history demonstrated that white rot and intact tissue contents are key measurements in evaluating vines’ sanitary status. We finally proposed a model for an accurate trunk disease diagnosis in grapevine. This work opens new routes for precision agriculture andin-situmonitoring of wood quality and plant health across plant species.

Published
2022

9. Characterization of genetic determinants of the resistance to phylloxera, Daktulosphaira vitifoliae, and the dagger nematode Xiphinema index from muscadine background

Author

Roger Voisin, Benjamin Joubard, Loïc Le Cunff, Daniel Esmenjaud, Pierre-François Bert, Daciana Papura, Jean-Pascal Tandonnet, Martine Donnart, Nathalie Ollat, Bernadette Rubio, Ulysse Portier, Guillaume Lalanne-Tisné, Cyril Van Ghelder, Jean-Pierre Petit, Maria Lafargue, Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Santé et agroécologie du vignoble (UMR SAVE), Institut Français de la Vigne et du Vin (IFV), French Ministry of Agriculture through the CASDAR C-2014-09 EDP 09 16 00 2775EDP 09 17 00 3392EDP 09 18 00 3764, European Project: 311775,EC:FP7:KBBE,FP7-KBBE-2012-6-singlestage,INNOVINE(2013), and Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
0106 biological sciences, Genotype, Nematoda, Genetic Linkage, Nepovirus, Quantitative Trait Loci, Muscadine, Plant Science, Breeding, Quantitative trait locus, Polymorphism, Single Nucleotide, 01 natural sciences, Xiphinema index, Hemiptera, 03 medical and health sciences, Genetic linkage, lcsh:Botany, Genetic architecture, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Vitis, Phylloxera, Disease Resistance, Plant Diseases, 030304 developmental biology, Nematode, Genetics, 0303 health sciences, biology, Bulked segregant analysis, Chromosome Mapping, food and beverages, Grapevine fanleaf virus, biology.organism_classification, lcsh:QK1-989, Pest resistance, Phenotype, Backcrossing, Grapevine, Rootstock, Lod Score, Research Article, Microsatellite Repeats, 010606 plant biology & botany
Abstract

Background Muscadine (Muscadinia rotundifolia) is known as a resistance source to many pests and diseases in grapevine. The genetics of its resistance to two major grapevine pests, the phylloxera D. vitifoliae and the dagger nematode X. index, vector of the Grapevine fanleaf virus (GFLV), was investigated in a backcross progeny between the F1 resistant hybrid material VRH8771 (Vitis-Muscadinia) derived from the muscadine R source ‘NC184–4’ and V. vinifera cv. ‘Cabernet-Sauvignon’ (CS). Results In this pseudo-testcross, parental maps were constructed using simple-sequence repeats markers and single nucleotide polymorphism markers from a GBS approach. For the VRH8771 map, 2271 SNP and 135 SSR markers were assembled, resulting in 19 linkage groups (LG) and an average distance between markers of 0.98 cM. Phylloxera resistance was assessed by monitoring root nodosity number in an in planta experiment and larval development in a root in vitro assay. Nematode resistance was studied using 10–12 month long tests for the selection of durable resistance and rating criteria based on nematode reproduction factor and gall index. A major QTL for phylloxera larval development, explaining more than 70% of the total variance and co-localizing with a QTL for nodosity number, was identified on LG 7 and designated RDV6. Additional QTLs were detected on LG 3 (RDV7) and LG 10 (RDV8), depending on the in planta or in vitro experiments, suggesting that various loci may influence or modulate nodosity formation and larval development. Using a Bulked Segregant Analysis approach and a proportion test, markers clustered in three regions on LG 9, LG 10 and LG 18 were shown to be associated to the nematode resistant phenotype. QTL analysis confirmed the results and QTLs were thus designated respectively XiR2, XiR3 and XiR4, although a LOD-score below the significant threshold value was obtained for the QTL on LG 18. Conclusions Based on a high-resolution linkage map and a segregating grapevine backcross progeny, the first QTLs for resistance to D. vitifoliae and to X. index were identified from a muscadine source. All together these results open the way to the development of marker-assisted selection in grapevine rootstock breeding programs based on muscadine derived resistance to phylloxera and to X. index in order to delay GFLV transmission.

Published
2020

10. Across-population genomic prediction in grapevine opens up promising prospects for breeding

Author

Vincent Segura, Agnès Doligez, Jean-Pierre Péros, Loïc Le Cunff, Patrice This, Thierry Pons, Pierre François, Timothée Flutre, and Charlotte Brault

Subjects
education.field_of_study, Training set, Population, Plant Science, Mating design, Horticulture, Heritability, Biology, Biochemistry, Genetic distance, Statistics, Genetics, Vitis vinifera, education, Selection (genetic algorithm), Genomic selection, Biotechnology
Abstract

Crop breeding involves two selection steps: choosing progenitors and selecting offspring within progenies. Genomic prediction, based on genome-wide marker estimation of genetic values, could facilitate these steps. However, its potential usefulness in grapevine (Vitis viniferaL.) has only been evaluated in non-breeding contexts mainly through cross-validation within a single population. We tested across-population genomic prediction in a more realistic breeding configuration, from a diversity panel to ten bi-parental crosses connected within a half-diallel mating design. Prediction quality was evaluated over 15 traits of interest (related to yield, berry composition, phenology and vigour), for both the average genetic value of each cross (cross mean) and the genetic values of individuals within each cross (individual values). Genomic prediction in these conditions was found useful: for cross mean, average per-trait predictive ability was 0.6, while per-cross predictive ability was halved on average, but reached a maximum of 0.7. Mean predictive ability for individual values within crosses was 0.26, about half the within-half-diallel value taken as a reference. For some traits and/or crosses, these across-population predictive ability values are promising for implementing genomic selection in grapevine breeding. This study also provided key insights on variables affecting predictive ability. Per-cross predictive ability was well predicted by genetic distance between parents and when this predictive ability was below 0.6, it was improved by training set optimization. For individual values, predictive ability mostly depended on trait-related variables (magnitude of the cross effect and heritability). These results will greatly help designing grapevine breeding programs assisted by genomic prediction.

Published
2022

11. A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

Author

Timothée Flutre, Loïc Le Cunff, Agota Fodor, Amandine Launay, Charles Romieu, Gilles Berger, Yves Bertrand, Nancy Terrier, Isabelle Beccavin, Virginie Bouckenooghe, Maryline Roques, Lucie Pinasseau, Arnaud Verbaere, Nicolas Sommerer, Véronique Cheynier, Roberto Bacilieri, Jean-Michel Boursiquot, Thierry Lacombe, Valérie Laucou, Patrice This, Jean-Pierre Péros, and Agnès Doligez

Subjects
Plant Breeding, Phenotype, Quantitative Trait Loci, Genetics, food and beverages, Chromosome Mapping, Molecular Biology, Polymorphism, Single Nucleotide, Genetics (clinical), Genome-Wide Association Study
Abstract

To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.

Published
2022

12. Genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

Author

Timothée Flutre, Loïc Le Cunff, Agota Fodor, Amandine Launay, Charles Romieu, Gilles Berger, Yves Bertrand, Nancy Terrier, Isabelle Beccavin, Virginie Bouckenooghe, Maryline Roques, Lucie Pinasseau, Arnaud Verbaere, Nicolas Sommerer, Véronique Cheynier, Roberto Bacilieri, Jean-Michel Boursiquot, Thierry Lacombe, Valérie Laucou, Patrice This, Jean-Pierre Péros, and Agnès Doligez

Subjects
Evolutionary biology, Genotype, Genetic variation, Trait, food and beverages, Single-nucleotide polymorphism, Genome-wide association study, Heritability, Quantitative trait locus, Biology, Genetic architecture
Abstract

To cope with the challenges faced by agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait locus (QTL) in bi-parental crosses, we exploited a diverse panel of 279 Vitis vinifera L. cultivars. This panel planted in five blocks in the vineyard was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms (SNPs) by combining an 18K microarray and genotyping-by-sequencing (GBS). The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. Overall, 489 reliable QTLs were detected for 41% more response variables than by a SNP-by-SNP model with microarray-only SNPs, many new ones compared to the results from bi-parental crosses. Prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as QTL and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application in breeding are discussed.

Published
2020

13. Quantitative Assessment of Grapevine Wood Colonization by the Dieback Fungus Eutypa lata

Author

Gilles Berger, Loïc Le Cunff, Jean-Pierre Péros, Timothée Flutre, Cédric Moisy, Géno-vigne® (UMT Géno-vigne®), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, 0301 basic medicine, Microbiology (medical), vignoble, Eutypa lata, Vegetative reproduction, Plant Science, Fungus, fungus, pathogenicity, susceptibility, real-time PCR, Vitis vinifera, wood colonization, vineyard, 01 natural sciences, Vineyard, maladie fongique, Article, 03 medical and health sciences, Cutting, fungal diseases, Botany, amplification par pcr, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Colonization, Cultivar, degré de sensibilité, Ecology, Evolution, Behavior and Systematics, Vegetal Biology, biology, Inoculation, symptôme, food and beverages, biology.organism_classification, symptom, grapevine, Horticulture, 030104 developmental biology, vigne, Pruning, Biologie végétale, 010606 plant biology & botany, pathogen, agent pathogène
Abstract

UMR AGAP Equipe Diversité, adaptation et amélioration de la vigne (DAAV); Eutypa lata is a fungal pathogen causing severe dieback in vineyards worldwide. This fungus colonizes vines through pruning wounds, eventually causing a brown sectorial necrosis in wood as well as stunted vegetative growth. Several years may pass between infection and the expression of external symptoms, hindering the rapid evaluation of both grapevine cultivars susceptibility and E. lata variation in aggressiveness. We aimed to develop a rapid quantitative method for the assessment of wood colonization after inoculation of cuttings in controlled conditions. We used several grape cultivars varying in susceptibility in the vineyard and fungal isolates with different levels of aggressiveness to monitor wood colonization during a maximum period of 2 months. Re-isolation allowed demonstration of the effects of both cultivars and fungal isolates on the rate of wood colonization. We also developed a real-time PCR method that was efficient in measuring fungal biomass, which was found to be correlated with isolate aggressiveness based on foliar symptom severity. The real-time PCR approach appears to be a useful technology to evaluate grapevine susceptibility to E. lata, and could be adapted to other pathogens associated with grapevine trunk diseases.

Published
2017

14. Developmental, molecular and genetic studies on grapevine response to temperature open breeding strategies for adaptation to warming

Author

Yannick Sire, Charles Romieu, Hernán Ojeda, Patrice This, Jérémie Pillet, Markus Rienth, Fatma Lecourieux, Cléa Houel, Mélanie Veyret, Jean Pierre Péros, Loïc Le Cunff, Ratthaphon Chatbanyong, Catherine Roux, Antoine Bigard, Nathalie Luchaire, Anne Pellegrino, Philippe Pieri, David Lecourieux, Marc Farnos, Emmanuelle Zumstein, Rezth Shahood, Laurent Torregrosa, Bertrand Muller, Nicolas Saurin, Angélique Adivèze, Agnès Doligez, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut Français de la Vigne et du Vin (IFV), Unité expérimentale de Pech-Rouge, Institut National de la Recherche Agronomique (INRA), Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut des Sciences de la Vigne et du Vin (ISVV)-Université de Bordeaux (UB), Fondation Jean Poupelain, Changins Haute Ecole de Viticulture et Oenologie, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut des Sciences de la Vigne et du Vin [Villenave d'Ornon] (ISVV), Université de Bordeaux (UB), Géno-vigne® (UMT Géno-vigne®), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA), ANR-2010-GENM-004-01, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité expérimentale de Pech-Rouge (PECH ROUGE), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), 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 Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA), ANR-10-GENM-0004,DURAVITIS,Bases développementales, moléculaires et génétiques de l'adaptation de la vigne à la contrainte thermique.(2010), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Torregrosa, Laurent, Diversité et adaptation des plantes cultivées (UMR DIAPC), 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), Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Mathématiques de Marseille (I2M), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Unité d'oenologie de Pech-Rouge (MONTP PECH ROUG UE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Vegetative reproduction, Berry, adaptation, 01 natural sciences, heat stress, Cutting, lcsh:Botany, Cultivar, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, 0303 health sciences, Vegetal Biology, genetic improvement, Ecology, biology, Global warming, food and beverages, Ripening, lcsh:QK1-989, Agricultural sciences, écophysiologie végétale, stress thermique, Vine, cartographie de qtl, Quantitative trait locus, Biology, Horticulture, lcsh:Agriculture, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, analyse génomique, 030304 developmental biology, business.industry, lcsh:S, temperature, 15. Life on land, Biotechnology, grapevine, 030104 developmental biology, adaptation au changement climatique, Adaptation, business, vigne, Biologie végétale, Sciences agricoles, 010606 plant biology & botany, Food Science
Abstract

Aim: In the long term, genetic improvement is one of the major strategies to support sustainable wine production in a changing climate. Over the past 5 years, we have developed an interdisciplinary research program that aimed to: i) characterize the impact of temperature increase sensed by the entire plant or individual bunches on the development and functioning of the plant, ii) identify the physiological and molecular mechanisms regulating the response of vegetative and reproductive development to heat stress and iii) develop tools to map quantitative trait loci (QTLs) of plant and berry development in duly controlled, stable, and contrasting environmental conditions.Methods and results: Performing high-throughput genomic analyses combined with the use of innovative experimental designs (fruiting cuttings, microvines, single berry sampling) was critical to decipher the ecophysiological and molecular mechanisms involved in the vine response to high temperature.Conclusion: Warming promotes vegetative growth and hampers plant carbon balance, disturbing flower set and young berry development. High temperatures modify primary and secondary fruit metabolisms, desynchronizing sugar and organic acid metabolisms and delaying sugar and polyphenol accumulation during ripening. The study of day and night transcriptomic and proteomic signatures associated with heat highlighted key players of the response to temperature in the fruit. Significance and impact of the study: Capitalizing on this knowledge, a new program is being proposed for the selection of cultivars limiting the accumulation of sugars in the berry while maintaining other qualitative compounds.

Published
2017

15. Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

Author

Roberto Bacilieri, Valérie Laucou, Loïc Le Cunff, Frédéric Martins, Amandine Launay, Stéphane Nicolas, Sophie Valière, Agnès Doligez, Aurélie Bérard, Marie-Christine Le Paslier, Alexis Dereeper, Jean-Pierre Péros, Brigitte Mangin, Thierry Lacombe, Patrice This, Philippe Chatelet, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Géno-vigne® (UMT Géno-vigne®), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), ANR-08-GENM-0002,DLVitis,Structure génétique et déséquilibre de liaison chez 3 espèces du genre Vitis(2008), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes végétaux - EPGV [Evry], Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de Génotypage (CNG), Unité Mathématiques et Informatique Appliquées de Toulouse (MIAT), GeT PlaGe, Genotoul, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BMC, BMC, Génomique - Structure génétique et déséquilibre de liaison chez 3 espèces du genre Vitis - - DLVitis2008 - ANR-08-GENM-0002 - GENM - VALID, 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 des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA), Doligez, Agnes, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de Génotypage ( CNG ), Unité Mathématiques et Informatique Appliquées de Toulouse ( MIAT ), Institut National de la Recherche Agronomique ( INRA ), Institut des Maladies Métaboliques et Cardiovasculaires ( I2MC ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Hôpital de Rangueil-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Géno-vigne® ( UMT Géno-vigne® ), Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ) -Institut National de la Recherche Agronomique ( INRA ) -Institut Français de la Vigne et du Vin (IFV), UMR - Interactions Plantes Microorganismes Environnement ( UMR IPME ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), and ANR-08-GENM-0002,DLVitis,Structure génétique et déséquilibre de liaison chez 3 espèces du genre Vitis ( 2008 )

Subjects
0106 biological sciences, 0301 basic medicine, Linkage disequilibrium, [SDV]Life Sciences [q-bio], Genome-wide association study, Plant Science, polymorphisme, 01 natural sciences, Genome-wide association studies, Haplotype, Vitis, sylvestris, Association mapping, 2. Zero hunger, Genetics, changement climatique, Vegetal Biology, Vassal collection, Tag SNP, [SDV] Life Sciences [q-bio], Phenotype, diversité génétique, Kinship, Gene pool, génotype, Research Article, Genetic Markers, Association panel, Genotype, SNP, Biology, Genes, Plant, Polymorphism, Single Nucleotide, 03 medical and health sciences, Species Specificity, Genetic variation, Genetic association, Genetic diversity, vitis, association panel, linkage disequilibrium, power, genome-wide association studies, SSR, haplotype, kinship, [ SDV ] Life Sciences [q-bio], Genetic Variation, 030104 developmental biology, 13. Climate action, Power, vigne, Biologie végétale, Genome-Wide Association Study, 010606 plant biology & botany, cultivar
Abstract

Background As for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies. Results Starting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance). Conclusions Our association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0754-z) contains supplementary material, which is available to authorized users.

Published
2016

16. VvGAI1 polymorphisms associate with variation for berry traits in grapevine

Author

Loïc Le Cunff, M. Teresa de Andrés, Patrice This, Alba M. Vargas, Javier Ibáñez, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Géno-vigne® (UMT Géno-vigne®), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA), Universidad de La Rioja-Gobierno de La Rioja, Spanish National Research Council (CSIC), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Genome Canada, Fundación Genoma España, Ministerio de Ciencia e Innovación (España), Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Linkage disequilibrium, [SDV]Life Sciences [q-bio], Plant Science, Berry, Association analysis, Horticulture, Biology, 01 natural sciences, 03 medical and health sciences, Botany, Genetics, Gene, 030304 developmental biology, Genetic association, 2. Zero hunger, 0303 health sciences, Table grape, Haplotype, food and beverages, association analysis, VvGAI1, table grape, Vitis vinifera, Genetic structure, Gibberellin, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Gibberellins have important effects over different developmental processes in plants and the exogenous application of GA3 has been extensively used in grapevine to improve certain quality traits (to control berry size, set and weight, to decrease cluster compactness and to induce the absence of seeds in grapes). In this study, we performed association analyses using a core collection of 127 table grape accessions in order to identify causal SNPs in the gene VvGAI1, a negative regulator of gibberellins response. Seventeen quantitative descriptors, related with fertility, bunch and berry traits were used for the association analysis with VvGAI1. Fifteen polymorphisms and 15 haplotypes were identified, and some of them associated significantly with important traits for table grape: berry texture, juice yield, and bunch weight. The genetic structure found in the collection of varieties was consistent with their origins, and was included in the association test. In addition, nucleotide and haplotypic diversity, linkage disequilibrium and the possible existence of selection over the gene were also evaluated to support the association test. © 2013 Springer Science+Business Media Dordrecht., This study was made possible with the funding from the GrapeGen Project (joint venture between Genome Canada and Genoma España), and the AGL2010-15694 from the MICINN (Spain). A.M. Vargas was funded by a predoctoral fellowship from IMIDRA.

Published
2013

17. Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars

Author

Loïc Le Cunff, Angélique D'Hont, Lyonel Toubi, Yves Rousselle, Laurent Costet, Stefan Royaert, Louis-Marie Raboin, Hugues Telismart, Olivier Garsmeur, Jean-Yves Hoarau, Jérôme Pauquet, Catherine Hervouet, Jean-Christophe Glaszmann, Samuel Nibouche, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, Résistance génétique, [SDV]Life Sciences [q-bio], Sélection, Polymerase Chain Reaction, 01 natural sciences, Rust, Linkage Disequilibrium, F30 - Génétique et amélioration des plantes, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Puccinia melanocephala, Marqueur génétique, Cultivar, 0303 health sciences, biology, Chromosome Mapping, food and beverages, General Medicine, Major gene, Saccharum, PCR, Rouille, Biotechnology, Genetic Markers, DNA, Plant, Fungus, Genes, Plant, Chromosomes, Plant, 03 medical and health sciences, Polyploid, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Variété, Plant Diseases, H20 - Maladies des plantes, 030304 developmental biology, Basidiomycota, Haplotype, Résistance aux maladies, biology.organism_classification, Immunity, Innate, Haplotypes, Gène, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

International audience; Modern sugarcane cultivars (Saccharum spp., 2n = 100–130) are high polyploid, aneuploid and of interspecific origin. A major gene (Bru1) conferring resistance to brown rust, caused by the fungus Puccinia melanocephala, has been identified in cultivar R570. We analyzed 380 modern cultivars and breeding materials covering the worldwide diversity with 22 molecular markers genetically linked to Bru1 in R570 within a 8.2 cM segment. Our results revealed a strong LD in the Bru1 region and strong associations between most of the markers and rust resistance. Two PCR markers, that flank the Bru1-bearing segment, were found completely associated with one another and only in resistant clones representing efficient molecular diagnostic for Bru1. On this basis, Bru1 was inferred in 86 % of the 194 resistant sugarcane accessions, revealing that it constitutes the main source of brown rust resistance in modern cultivars. Bru1 PCR diagnostic markers should be particularly useful to identify cultivars with potentially alternative sources of resistance to diversify the basis of brown rust resistance in breeding programs.

Published
2012

18. Haplotype diversity of VvTFL1A gene and association with cluster traits in grapevine (V. vinifera)

Author

Loïc Le Cunff, José M. Martínez-Zapater, Thierry Lacombe, Patrice This, Lucie Fernandez, Sandrine Lalet, Laurent Torregrosa, Jean Michel Boursiquot, Javier Tello, Gema Bravo, Alexandre Fournier-Level, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Instituto de Ciencias de la Vid y el Vino (ICVV), Universidad de La Rioja (UR), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Bio21 Institute, Department of Genetics, University of Melbourne, Dpto. de Genética Molecular de Plantas, National Centre of Biotechnology (CNB), UE 1057 Domaine Expérimental de Vassal, Institut National de la Recherche Agronomique (INRA)-Biologie et Amélioration des Plantes (BAP)-Domaine Expérimental de Vassal (VASSAL), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), European Commission, Universidad de La Rioja (UR)-Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Linkage disequilibrium, Flowering time, Inflorescence structure, Plant Science, Biology, Genes, Plant, Haplogroup, Nucleotide diversity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Vitis, Allele, Indel, Flowering Tops, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Berry size, Genetic association, 2. Zero hunger, Genetics, Genetic diversity, Polymorphism, Genetic, Vegetal Biology, Haplotype, Plant reproductive development, Grape domestication, Grapevine, Biologie du développement, food and beverages, Sequence Analysis, DNA, croatie, Development Biology, Agricultural sciences, cépage, Haplotypes, génotype, vigne, Sciences agricoles, Biologie végétale, Research Article
Abstract

Fernandez, Lucie et al., [Background] Interaction between TERMINAL FLOWER 1 (TFL1) and LEAFY (LFY) seem to determine the inflorescence architecture in Arabidopsis. In a parallel way, overexpression of VvTFL1A, a grapevine TFL1 homolog, causes delayed flowering and production of a ramose cluster in the reiterated reproductive meristem (RRM) somatic variant of cultivar Carignan. To analyze the possible contribution of this gene to cluster phenotypic variation in a diversity panel of cultivated grapevine (Vitis vinifera L. subsp. vinifera) its nucleotide diversity was characterized and association analyses among detected sequence polymorphisms and phenology and cluster traits was carried out., [Results] A total of 3.6 kb of the VvTFL1A gene, including its promoter, was sequenced in a core collection of 140 individuals designed to maximize phenotypic variation at agronomical relevant traits. Nucleotide variation for VvTFL1A within this collection was higher in the promoter and intron sequences than in the exon regions; where few polymorphisms were located in agreement with a high conservation of coding sequence. Characterization of the VvTFL1A haplotype network identified three major haplogroups, consistent with the geographic origins and the use of the cultivars that could correspond to three major ancestral alleles or evolutionary branches, based on the existence of mutations in linkage disequilibrium. Genetic association studies with cluster traits revealed the presence of major INDEL polymorphisms, explaining 16%, 13% and 25% of flowering time, cluster width and berry weight, respectively, and also structuring the three haplogroups., [Conclusions] At least three major VvTFL1A haplogroups are present in cultivated grapevines, which are defined by the presence of three main polymorphism LD blocks and associated to characteristic phenotypic values for flowering time, cluster width and berry size. Phenotypic differences between haplogroups are consistent with differences observed between Eastern and Western grapevine cultivars and could result from the use of different genetic pools in the domestication process as well as different selection pressures on the development of table and wine cultivars, respectively. Altogether, these results are coherent with previous classifications of grapevine phenotypic diversity mainly based on cluster and berry morphotypes as well as with recent results on the structure of genetic diversity in cultivated grapevine. © 2014 Fernandez et al., This work was funded by grant BIO2008-03892 and BIO2011-026229 from the MICINN and MINECO of Spain to JMM-Z. Networking activities were also funded by COST Action FA1003 “East–west Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding”. JT was recipient of a fellowship from the MICINN.

Published
2014

19. Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine

Author

Agota Fodor, Loïc Le Cunff, Philippe Chatelet, Félix Abdel Aziz Homa, Marie Denis, Thierry Lacombe, Patrice This, Samuel Neuenschwander, Vincent Segura, Alexandre Fournier-Level, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Institut National de la Recherche Agronomique (INRA), Department of Ecology and Evolution, Université de Lausanne (UNIL), Swiss Institute of Bioinformatics, Vital-IT, Department of Genetics, University of Melbourne, Swiss National Science Foundation grant 31003A_138180 to Dr. J. Goudet. French Ministry of Research and Higher Education and the French Ministry of Food, Agriculture and Fisheries (project CAS DAR n u10AAPIT n u1009). PhD grant from the French Grapevine and Wine Institute (IFV)., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF)

Subjects
0106 biological sciences, cartographie génomique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Agricultural Biotechnology, marqueur génomique, Selection Markers, lcsh:Medicine, Population genetics, Breeding, 01 natural sciences, Linkage Disequilibrium, F30 - Génétique et amélioration des plantes, genomic selection, GWAS, Vitis, Statistical Analysis of Genetic Association, lcsh:Science, 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Agriculture, Biodiversity, Biological Evolution, Phenotype, genome wide, association study, Quantitative Trait Association Studies, Research Article, Heterozygote, Marker-Assisted Selection, Quantitative Trait Loci, Population, Genomics, Context (language use), Biotechnologies, Computational biology, Biology, Quantitative trait locus, Research and Analysis Methods, 03 medical and health sciences, vitis vinifera, Quantitative Trait, Heritable, Genome-Wide Association Studies, valeur phénotypique, Computer Simulation, donnée génomique, sélection génomique, Selection, Genetic, Family-Based Association Studies, Molecular Biology Techniques, education, Molecular Biology, Genetic Association Studies, Selection (genetic algorithm), 030304 developmental biology, Genetic diversity, Models, Statistical, Models, Genetic, lcsh:R, Reproducibility of Results, Biology and Life Sciences, Computational Biology, étude d'association pangénomique, Marker Genes, Genome Analysis, Genetic architecture, modèle prédictif, détection de qtl, lcsh:Q, Genome-Wide Association Study, 010606 plant biology & botany
Abstract

INRA UMR 1334 AGAP, Equipe DAVEM = Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.

Published
2014

20. An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods

Author

Christine Dubreuil-Tranchant, Patrice This, Marguerite Rodier-Goud, Gregory Carrier, Alexandre de Kochko, Sylvain Santoni, Loïc Le Cunff, Jean-Michel Boursiquot, Aurélie Canaguier, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Géno-vigne® (UMT Géno-vigne®), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Diversité et adaptation des plantes cultivées (UMR DIAPC), 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), Diversité et Adaptation des Plantes Cultivées, Institut de Recherche pour le Développement (IRD [ Madagascar]), Développement et amélioration des plantes (UMR DAP), 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), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1097 Diversité et Adaptation des Plantes Cultivées, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), 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), 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), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Cytoplasm, caféier, nuclei isolation, Plant Science, dna, Coffee, 01 natural sciences, F30 - Génétique et amélioration des plantes, séquenceurs de nouvelle génération, chemistry.chemical_compound, Vitis, 2. Zero hunger, 0303 health sciences, next generation sequencers, adn, coffee tree, viticulture, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Nuclear DNA, DNA Contamination, isolation, Nucleic Acid Amplification Techniques, Genome, Plant, Méthodologie, coffea, DNA, Plant, Molecular Sequence Data, fruit tree, Computational biology, Biology, fruit arboriculture, DNA sequencing, 03 medical and health sciences, Coffea canephora, vitis vinifera, séquençage, Genetics, Gene, Ecology, Evolution, Behavior and Systematics, Gene Library, nuclear plant DNA extraction, arbre fruitier, 030304 developmental biology, Cell Nucleus, Bacterial artificial chromosome, Base Sequence, business.industry, gène, Multiple displacement amplification, Sequence Analysis, DNA, DNA extraction, grapevine, Biotechnology, isolement des noyaux, arboriculture fruitière, chemistry, nuclei, extraction, extraction de l'ADN nucléaire des plantes, vigne, business, DNA, 010606 plant biology & botany
Abstract

All protocols for Next Generation Sequencers (NGS) start with the preparation of a DNA library from extracted DNA. Quality, number, and length of the sequences produced by NGS all depend on the quality of the library that was prepared, itself dependent on the DNA quality. Generally, when using NGS, one would wish to obtain the genomic information contained in the nucleus without an excessive proportion of cytoplasmic DNA. Multiple copies of cytoplasmic genomes are present in every cell (11 to 70 copies, depending on the developmental stage and/or physiological status) ( Tymms et al., 1983 ). The chloroplast DNA of plants, therefore, represents 17 - 23% of their total DNA ( Boffey and Leech, 1982 ). In this study, we developed a protocol that strongly reduces the amount of cytoplasmic DNA. The improvement in quality makes the method perfectly adapted to library construction for NGS. We applied this extraction method to the grapevine ( Vitis vinifera L.) and coffee tree ( Coffea canephora Pierre ex A. Froehner). These species are known to contain many secondary metabolites, which can generate diffi culties for DNA extraction ( Peterson et al., 1997 ; Mattivi et al., 2006 ). To establish the protocol, we were partially inspired by a classic protocol for nuclear DNA plant extraction destined for the construction of BAC (Bacterial Artifi cial Chromosome) libraries ( Peterson et al., 1997 ). The two stages of the protocol are: (i) isolation of nuclei and (ii) nuclear DNA extraction. Nuclear DNA obtained with this protocol was then sequenced using 454/GS-FLX technology (Roche, Basel, Switzerland) with the Titanium kit. All protocols for Next Generation Sequencers (NGS) start with the preparation of a DNA library from extracted DNA. Quality, number, and length of the sequences produced by NGS all depend on the quality of the library that was prepared, itself dependent on the DNA quality. Generally, when using NGS, one would wish to obtain the genomic information contained in the nucleus without an excessive proportion of cytoplasmic DNA. Multiple copies of cytoplasmic genomes are present in every cell (11 to 70 copies, depending on the developmental stage and/or physiological status) ( Tymms et al., 1983 ). The chloroplast DNA of plants, therefore, represents 17 - 23% of their total DNA ( Boffey and Leech, 1982 ). In this study, we developed a protocol that strongly reduces the amount of cytoplasmic DNA. The improvement in quality makes the method perfectly adapted to library construction for NGS. We applied this extraction method to the grapevine ( Vitis vinifera L.) and coffee tree ( Coffea canephora Pierre ex A. Froehner). These species are known to contain many secondary metabolites, which can generate diffi culties for DNA extraction ( Peterson et al., 1997 ; Mattivi et al., 2006 ). To establish the protocol, we were partially inspired by a classic protocol for nuclear DNA plant extraction destined for the construction of BAC (Bacterial Artifi cial Chromosome) libraries ( Peterson et al., 1997 ). The two stages of the protocol are: (i) isolation of nuclei and (ii) nuclear DNA extraction. Nuclear DNA obtained with this protocol was then sequenced using 454/GS-FLX technology (Roche, Basel, Switzerland) with the Titanium kit.

Published
2010

21. Selection of candidate genes for grape proanthocyanidin pathway by an integrative approach

Author

Nancy Terrier, Véronique Cheynier, Jean-Marc Souquet, Patrice This, Loïc Le Cunff, Alexandre Fournier-Level, Sandrine Vialet, Yung-Fen Huang, Gregory Carrier, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), French Ministry of Research and Higher Education, French Ministry of Food, Agriculture and Fisheries, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, Vitis vinifera L, Physiology, Proanthocyanidin biosynthesis, Plant Science, Computational biology, Biology, Quantitative trait locus, Bioinformatics, 01 natural sciences, Candidate genes, Transcriptome, 03 medical and health sciences, Gene Expression Regulation, Plant, expression, Screening method, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Proanthocyanidins, Vitis, genetics, Transcriptomics, carboxypeptidase-like protein, Gene, genome, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, secondary metabolism, tea catechins, lipid bilayers, vitis-vinifera, association, QTLs, arabidopsis, Proanthocyanidin, Molecular physiology, identification, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Signal Transduction, 010606 plant biology & botany
Abstract

Proanthocyanidins (PA) play a major role in plant protection against biotic and abiotic stresses. Moreover these molecules are known to be beneficial for human health and are responsible for astringency of foods and beverages such as wine and thus have a great impact on the final quality of the product. Genes playing a role in the PA pathway are only partially known. The amount of available transcriptomic and genetic data to select candidate genes without a priori knowledge from orthologous function increases every day. However, the methods used so far generate so many candidate genes that it is impossible to validate all of them. In this study, we used an integrative strategy based on different screening methods to select a reduced list of candidate genes. We have crossed results from different screening methods including QTL mapping and three transcriptomic studies to select 20 candidate genes, located in QTL intervals and fulfilling at least two transcriptomic screenings. This list includes three glucosyltransferases, already suspected to have a role in the PA biosynthetic pathway. Among the 17 remaining genes, we selected three genes to perform further analysis by association genetic studies. For each of these genes, we found a polymorphism linked to PA variation. The three genes (VvMybC2-L1, VvGAT-like and VvCob-like), not previously known to play a role in PA synthesis, are promising candidates for further molecular physiology studies.

Published
2013

22. Characterization of single nucleotide polymorphism in Tunisian grapevine genome and their potential for population genetics and evolutionary studies

Author

Alexandre Fournier-Level, Ahmed Mliki, Nejia Zoghlami, Valérie Laucou, Loïc Le Cunff, Leila Riahi, Alexis Dereeper, Patrice This, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), INRA, Montpellier France, Tunisian Ministry of Higher Education, Scientific Research and Technology, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Vitis vinifera L, Tunisia, Population genetics, Plant Science, Biology, 01 natural sciences, polymorphism, Nucleotide diversity, Gene flow, 03 medical and health sciences, Genetic relationships, haplotype diversity, genetic relationships, single nucleotide polymorphism, Genetics, Single nucleotide, Domestication, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, UPGMA, Haplotype diversity, Genetic structure, Gene pool, Selective sweep, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

In this study, two gene fragments corresponding to the VvMYBA1 and VvMYBA2 loci were sequenced on a sample of grapes including cultivated and wild accessions originating from Tunisia, Germany and France. A total of 42 SNPs were detected in the sequenced fragments giving an average of 1 SNP every 33 bp. High level of polymorphism was observed in the samples either in cultivated or wild accessions. Pattern of nucleotide diversity indicates a non departure from neutrality expectations for wild grapevine sample for gene VvMYBA1 and VvMYBA2 and for cultivated sample for gene VvMYBA1. However, a linkage to a selective sweep was revealed for cultivated grapevine gene pool in gene VvMYBA2. A genetic structure of the studied sample according to accession taxonomic status was revealed by the UPGMA clustering with a considerable overlap. This result was confirmed by significant but low genetic differentiation values between cultivated and wild sample. The number of migrants Nm based on sequence data information between Tunisian cultivars and Tunisian wild accessions showed a low level of gene flow between those germplasms. This finding indicates that Tunisian cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced during historical times. However, the possibility that some cultivars derived from ancestral events of local domestication or cross hybridization with native wild plants was not completely excluded for Tunisian grapevine accessions.

Published
2013

23. Genetic structure in cultivated grapevines is linked to geography and human selection

Author

Valérie Laucou, Blaise Genna, Roberto Bacilieri, Manuel Di Vecchi-Staraz, Jean-Pierre Péros, Thierry Lacombe, Patrice This, Loïc Le Cunff, Jean-Michel Boursiquot, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Domaine de Vassal, Institut National de la Recherche Agronomique (INRA), Domaine expérimental de Vassal (MONTP DOM VASSAL), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
0106 biological sciences, Genotype, [SDV]Life Sciences [q-bio], Plant Science, Biology, 01 natural sciences, Wine grape, 03 medical and health sciences, Genetic variation, Botany, Humans, Vitis, Cultivar, Domestication, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Geography, Table grape, fungi, Genetic Variation, food and beverages, 15. Life on land, Genetics, Population, Genetic structure, Microsatellite, 010606 plant biology & botany, Research Article
Abstract

Background - Grapevine (Vitis vinifera subsp. vinifera) is one of the most important and ancient horticultural plants in the world. Domesticated about 8--10,000 years ago in the Eurasian region, grapevine evolved from its wild relative (V. vinifera subsp. sylvestris) into very diverse and heterozygous cultivated forms. In this work we study grapevine genetic structure in a large sample of cultivated varieties, to interpret the wide diversity at morphological and molecular levels and link it to cultivars utilization, putative geographic origin and historical events. Results - We analyzed the genetic structure of cultivated grapevine using a dataset of 2,096 multi-locus genotypes defined by 20 microsatellite markers. We used the Bayesian approach implemented in the STRUCTURE program and a hierarchical clustering procedure based on Ward's method to assign individuals to sub-groups. The analysis revealed three main genetic groups defined by human use and geographic origin: a) wine cultivars from western regions, b) wine cultivars from the Balkans and East Europe, and c) a group mainly composed of table grape cultivars from Eastern Mediterranean, Caucasus, Middle and Far East countries. A second structure level revealed two additional groups, a geographic group from the Iberian Peninsula and Maghreb, and a group comprising table grapes of recent origins from Italy and Central Europe. A large number of admixed genotypes were also identified. Structure clusters regrouped together a large proportion of family-related genotypes. In addition, Ward's method revealed a third level of structure, corresponding either to limited geographic areas, to particular grape use or to family groups created through artificial selection and breeding. Conclusions - This study provides evidence that the cultivated compartment of Vitis vinifera L. is genetically structured. Genetic relatedness of cultivars has been shaped mostly by human uses, in combination with a geographical effect. The finding of a large portion of admixed genotypes may be the trace of both large human-mediated exchanges between grape-growing regions throughout history and recent breeding.

Published
2013

24. 3D modeling of metamaterials at oblique incidence and effective analysis

Author

Loïc Le Cunff, Alexandre Vial, Sylvain Blaize, Stéphane Collin, Anatole Lupu, Gilles Lerondel, Géno-vigne® (UMT Géno-vigne®), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Laboratoire de Nanotechnologie et d'Instrumentation Optique (LNIO), Institut Charles Delaunay (ICD), Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de photonique et de nanostructures (LPN), Centre National de la Recherche Scientifique (CNRS), Institut d'électronique fondamentale (IEF), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), and VU VAN, Jean-Baptiste

Subjects
[SPI.OPTI] Engineering Sciences [physics]/Optics / Photonic, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic
Abstract

International audience; The straightforward modeling of a metamaterial at its characteristic scale is a broad issue. The use of the “material” word implies that one can measure macroscopic quantities from it (such as an effective permittivity or an effective permeability). This approach has yet to be validated for any angle of incidence. The dependence of the refractive index on this angle becomes especially strong when the system is in the grazing incidence configuration, or as it starts guiding light. An effective model thus becomes of great importance if one wants to model the behavior of complex integrated devices based on metamaterials. The studies presented here have been done as part of the ANR METAPHOTONIQUE project, whose first purpose is to design metametarials operating on top of SOI guiding structures (Silicon on Insulator) at 1.55 micron. We present results of 3D simulations, done through the FDTD method, of a metamaterial of which the optical response has been computed at normal incidence and oblique incidence. We show that the full properties - the permittivity and permeability tensors - of such structures can be retrieved numerically thanks to that data and the use of optimization methods. We then study the range of validity of the effective index model, and if this model applies in the guided light configuration.

Published
2012

25. Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

Author

Yung-Fen Huang, Frédéric Véran, Loïc Le Cunff, Agnès Doligez, Cécile Morel, Yves Bertrand, Nancy Terrier, Alexandre Fournier-Level, Valérie Miralles, Véronique Cheynier, Aurélie Canaguier, Jean-Marc Souquet, Patrice This, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Sciences Pour l'Oenologie (SPO), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Department of Ecology and Evolutionary Biology, Brown University, Géno-vigne® (UMT Géno-vigne®), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, Candidate gene, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Plant Science, Berry, Biology, Quantitative trait locus, 01 natural sciences, Anthocyanidin reductase, 03 medical and health sciences, lcsh:Botany, Proanthocyanidins, Vitis, Cultivar, Allele, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Chromosome Mapping, food and beverages, Genetic architecture, lcsh:QK1-989, Epistasis, Research Article, 010606 plant biology & botany
Abstract

Background Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Results Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. Conclusions This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.

Published
2012

26. Highly polymorphic nSSR markers: A useful tool to assess origin of North African cultivars and to provide additional proofs of secondary grapevine domestication events

Author

Leila Riahi, Kaddour El-Heit, Nejia Zoghlami, Valérie Laucou, Ahmed Mliki, Loïc Le Cunff, Jean-Michel Boursiquot, Thierry Lacombe, Patrice This, Laboratoire de Physiologie Moléculaire des Plantes, Centre de Biotechnologie de Borj Cédria (Hammam-Lif, Tunisie), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Laboratoire d’Arboriculture et Viticulture, Département des Sciences Agronomiques, University of Tizi-Ouzou, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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, 0303 health sciences, Genetic diversity, Vitis vinifera L, Range (biology), [SDV]Life Sciences [q-bio], Horticulture, Biology, 01 natural sciences, cultivars origin, 03 medical and health sciences, domestication, nSSR markers, Evolutionary biology, Botany, Genetic structure, Microsatellite, Cultivar, Gene pool, Allele, Domestication, 030304 developmental biology, 010606 plant biology & botany
Abstract

Twenty highly polymorphic nuclear microsatellite markers were used to assess genetic relationships among 181 grapevine accessions traditionally grown in different geographical region of the species’ range and 21 wild Tunisian samples. A total of 330 alleles were detected and extensive genetic polymorphisms were recorded either in the cultivated or in the wild compartment. A genetic structure according to accessions taxonomic status and cultivars geographical origin was revealed by multivariate analysis and F st values. However, a considerable overlap was observed in the majority of distinguished groups. The highest level of differentiation between wild and cultivated accessions is recorded between Tunisian wild accessions and North African cultivars which are confirmed by multivariate analysis. Thus the occurrence of local domestication event of grapevines in the North African region is unlikely. North African cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced probably from East region or derived from crosses between them. A genetic affinity between wild gene pool and cultivars of West Europe was brought to light by multivariate and F st analysis. Pattern structure of genetic diversity in the analyzed material presents an additional proof of the occurrence of secondary grapevine domestication events in West Europe region which contributed to the evolution of the species, a hypothesis supported by recent archeobiological and molecular studies.

Published
2012

27. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L

Author

Jean-Michel Boursiquot, Alexis Dereeper, Loïc Le Cunff, Gregory Carrier, François Sabot, Patrice This, Olivier Bouchez, Laurent Audeguin, Delphine Legrand, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Carrier, Gregory, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], lcsh:Medicine, Plant Science, 01 natural sciences, Genome, polymorphism, Vitis, lcsh:Science, Phylogeny, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, Genomics, Plants, genome, phenotypic, snp, vitis vinifera l, sequence, Phenotype, Genome, Plant, Research Article, Cloning, Organism, Molecular Sequence Data, Single-nucleotide polymorphism, Context (language use), Biology, DNA sequencing, 03 medical and health sciences, Genetic Mutation, Genome Analysis Tools, Indel, 030304 developmental biology, Polymorphism, Genetic, Base Sequence, lcsh:R, Terminal Repeat Sequences, Sequence Analysis, DNA, DNA Transposable Elements, lcsh:Q, Mobile genetic elements, Sequence Alignment, Population Genetics, 010606 plant biology & botany, Reference genome
Abstract

Chantier qualité GA; Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.

Published
2012

28. Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine

Author

Loïc Le Cunff, Ximena Casanueva, María de los Ángeles Miccono, Rodrigo Ramos, Nilo Mejía, Marcos Guerrero, Jean Michel Boursiquot, Anne-Françoise Adam-Blondon, Patricio Hinrichsen, Braulio Soto, Cléa Houel, Instituto de Investigaciones Agropecuarias, 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Marie Curie Host Fellowship for Early Stage Research Training (EU program), Biofrutales S.A - Programa Bicentenario de Ciencia y Tecnologia - Conicyt, PBCT - Conicyt PSD-03, CORFO-INNOVA 08CT11PUD-07, FONDEFG07I1002, and Mejia, Nilo

Subjects
0106 biological sciences, Candidate gene, Transcription, Genetic, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Quantitative Trait Loci, MADS Domain Proteins, Single-nucleotide polymorphism, Locus (genetics), Plant Science, Quantitative trait locus, Biology, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, lcsh:Botany, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Coding region, Vitis, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Amino Acid Sequence, Promoter Regions, Genetic, Indel, Gene, Plant Proteins, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, fungi, Chromosome Mapping, food and beverages, Marker-assisted selection, lcsh:QK1-989, Seeds, Sequence Alignment, Research Article, 010606 plant biology & botany
Abstract

Background Stenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level. Results Genetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development. Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11's regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation. For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site. Conclusion We propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.

Published
2011

29. New insight into the genetics of color in grape

Author

Alexandre Fournier-Level, Loïc Le Cunff, Agnes Doligez, Patrice This, Agnès Ageorges, Véronique Cheynier, Jean-Marc Souquet, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Candidate gene, association genetics, QTL, [SDV]Life Sciences [q-bio], Population, Single-nucleotide polymorphism, genic markers, Horticulture, Biology, Quantitative trait locus, 01 natural sciences, anthocyanin, 03 medical and health sciences, chemistry.chemical_compound, MYB, education, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, food and beverages, Genetic architecture, White (mutation), chemistry, Anthocyanin, 010606 plant biology & botany
Abstract

Grapes may either be white or colored, ranging from the lightest pink to the darkest purple tone depending on the quantity and composition of anthocyanins accumulated in the berry skin. QTL mapping on cross-derived progeny and association mapping on natural diversity were combined to decipher the genetic architecture of anthocyanin content and composition in berry skin, a crucial trait for both wine quality and human nutrition. For the total anthocyanin content in the skin of mature berries on a segregating population of 191 progenies, we identified 2 QTLs accounting for 62% and 7.1% of the total variation. Further studying candidate genes from these QTL intervals on a core collection of natural resources (141 individuals), we identified Myb genes highly associated with total content of anthocyanins. Using a multivariate regression method, we demonstrated that four polymorphisms accounted for 86% of the observed variation, with all these polymorphisms leading to structural changes in the MYB proteins. Skin color tones are not only due to the overall pigment concentration but also to variation in pigment composition, mostly due to hydroxylation, methylation and acylation differences. For all these variations, the major QTL on LG2 played a key role. In addition, specific QTLs were found for each of the composition variable: on LG6, explaining 13% of the hydroxylation variation, on LG1, explaining up to 17% of the methylation variation and on LG7 and LG13, explaining 11 and 7% of the variation in p-coumaric acylation. For the hydroxylation level, the specific QTL on LG6 co-localized with candidate VvF3' 5' H genes and two genic SNPs within two of those genes were identified as associated to the variation. For the methylation variation, the specific QTL on LG1 co-localized with a cluster of O-methyltransferase genes among which VvAOMT3.2 showed a strong association.

Published
2010

30. Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp sativa) berry: A quantitative trait locus to quantitative trait nucleotide integrated study

Author

Agnès Doligez, Yves Bertrand, Loïc Le Cunff, Alexandre Fournier-Level, Véronique Cheynier, Agnès Ageorges, Jean-Marc Souquet, Camilla Gomez, Catherine Roux, Patrice This, Diversité et adaptation des plantes cultivées (UMR DIAPC), 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), Sciences Pour l'Oenologie (SPO), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Candidate gene, Genotype, SYRAH, Quantitative Trait Loci, Single-nucleotide polymorphism, Genome-wide association study, Wine, Quantitative trait locus, Biology, Investigations, Genes, Plant, 01 natural sciences, Polymorphism, Single Nucleotide, Linkage Disequilibrium, Anthocyanins, 03 medical and health sciences, Gene mapping, Genetic variation, Genetics, Vitis, REGRESSION MODEL, Association mapping, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Chromosome Mapping, Genetic Variation, food and beverages, Genetic architecture, QUANTITATIVE TRAIT LOCUS (QTL), NUCLEOTIDE POLYMORPHISM, Phenotype, Haplotypes, Fruit, Multivariate Analysis, GRENACHE, Regression Analysis, ANTHOCYANIN, BERRY, Genome, Plant, GRAPE, 010606 plant biology & botany, Genome-Wide Association Study, UNIGENE
Abstract

Correspondance auteur: This P. E-mail: this@supagro.inra.fr; International audience; The combination of QTL mapping studies of synthetic lines and association mapping studies of natural diversity represents an Opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping, which often leads to wide intervals encompassing numerous genes, it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape, a newly sequenced genome, to decipher the genetic architecture of anthocyanin content. Grapes may be either white or colored, ranging from die lightest pink to the darkest purple tones according to the amount of anthocyanin accumulated in the berry skin, which is a crucial trait. for both wine quality and human nutrition. Although the determinism of the white phenotype has been fully identified, the genetic bases of the quantitative variation of anthocyanin content in berry skin remain unclear. A single QTL responsible for up to 62% of the variation in the anthocyanin content was mapped on a Syrah X Grenache F-1 pseudo-testcross. Among the 68 unigenes identified in the grape genome within the QTL interval, a cluster of four Myb-type genes was selected on the basis of physiological evidence (VvMybA1, VvMybA2, VvMybA3, and VvMybA4). From a core collection of natural resources (141 individuals), 32 polymorphisms revealed significant association, and extended linkage disequilibrium was observed. Using a multivariate regression method, we demonstrated that five polymorphisms in VvMybA genes except. VvMybA4 (one retrotransposon, three single nucleotide polymorphisms and one 2-bp insertion/deletion) accounted for 84% of the observed variation. All these polymorphisms led to either structural changes in the MYB proteins or differences in the VvMybAs promoters. We concluded that the continuous variation in anthocyanin content in grape was explained mainly by a single gene cluster of three VvMybA genes. The rise of natural diversity helped to reduce one QTL to a set of five quantitative trait nucleotides and gave a clear picture of how isogenes combined their effects to shape grape color. Such analysis also illustrates how isogenes combine their effect to shape a complex quantitative trait and enables the definition of markers directly targeted for upcoming breeding programs

Published
2009

31. Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n approximately 12x approximately 115)

Author

Loïc, Le Cunff, Olivier, Garsmeur, Louis Marie, Raboin, Jérome, Pauquet, Hugues, Telismart, Athiappan, Selvi, Laurent, Grivet, Romain, Philippe, Dilara, Begum, Monique, Deu, Laurent, Costet, Rod, Wing, Jean Christophe, Glaszmann, and Angélique, D'Hont

Subjects
Genetic Markers, Chromosomes, Artificial, Bacterial, Models, Genetic, food and beverages, Oryza, Investigations, Aneuploidy, Genes, Plant, Physical Chromosome Mapping, Diploidy, Saccharum, Polyploidy, Chromosome Walking, Haplotypes, Cloning, Molecular, Sorghum, Plant Diseases
Abstract

The genome of modern sugarcane cultivars is highly polyploid (approximately 12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.

Published
2008

33. Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n ~ 12x ~ 115)

Author

Laurent Grivet, Loïc Le Cunff, Athiappan Selvi, Angélique D'Hont, Dilara Begum, Rod A. Wing, Louis Marie Raboin, Romain Philippe, Jean-Christophe Glaszmann, Jérôme Pauquet, Laurent Costet, Olivier Garsmeur, Monique Deu, Hugues Telismart, 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), Pôle de Protection des Plantes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Genomics Institute, Clemson University, Diversité et adaptation des plantes cultivées (UMR DIAPC), 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)-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), and 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)

Subjects
0106 biological sciences, Biology, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Polyploid, Nombre chromosomique, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Genetics, Primer walking, Puccinia melanocephala, Marqueur génétique, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, H20 - Maladies des plantes, 030304 developmental biology, Synteny, 2. Zero hunger, 0303 health sciences, Saccharum officinarum, Haplotype, Physical Chromosome Mapping, food and beverages, Résistance aux maladies, biology.organism_classification, Gène, Rouille, Carte génétique, Ploidy, 010606 plant biology & botany
Abstract

The genome of modern sugarcane cultivars is highly polyploid (∼12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.

Published
2008

34. Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones

Author

Loïc Le Cunff, Claire Lanaud, Xavier Sabau, Olivier Fouet, Jean-Christophe Glaszmann, Pietro Piffanelli, Didier Clément, E. Ruiz, and Ange-Marie Risterucci

Subjects
Genetic Markers, Phytophthora, Chromosomes, Artificial, Bacterial, Genotype, Theobroma, Moniliophthora roreri, Genomics, localisation de gène, Biology, Quantitative trait locus, Genome, Chromosomes, Plant, F30 - Génétique et amélioration des plantes, Contig Mapping, Genetics, Genomic library, Theobroma cacao, Gene, H20 - Maladies des plantes, Gene Library, Plant Diseases, clone, Cacao, Génome, food and beverages, Reproducibility of Results, General Medicine, biology.organism_classification, Résistance aux maladies, Physical Chromosome Mapping, Phenotype, Agronomy and Crop Science, Genome, Plant, Biotechnology
Abstract

We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

Published
2003

35. A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.)

Author

Loïc Le Cunff, Patrice This, Jean-Michel Boursiquot, F. Emanuelli, Juri Battilana, Maria Stella Grando, L. Costantini, Fondazione Edmund Mach, Research and Innovation Centre, Diversité et adaptation des plantes cultivées (UMR DIAPC), 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), UMT Génovigne, Institut Français de la Vigne et du Vin (IFV), and 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)

Subjects
0106 biological sciences, Linkage disequilibrium, Plant Science, 01 natural sciences, Linkage Disequilibrium, Gene Frequency, lcsh:Botany, Vitis, Aldose-Ketose Isomerases, Plant Proteins, 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, Vegetal Biology, food and beverages, raisin, lcsh:QK1-989, Settore AGR/07 - GENETICA AGRARIA, Taste, Oxidoreductases, Research Article, sélection végétale, Genotype, Molecular Sequence Data, Population, GENETIQUE, Locus (genetics), Quantitative trait locus, Biology, Genes, Plant, Polymorphism, Single Nucleotide, qualité organoleptique, 03 medical and health sciences, vitis vinifera, Species Specificity, Multienzyme Complexes, Genetic variation, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, education, 030304 developmental biology, Genetic association, Genetic diversity, Sequence Homology, Amino Acid, Table grape, Genetic Variation, création variétale, Haplotypes, Mutation, Monoterpenes, vigne, Biologie végétale, 010606 plant biology & botany
Abstract

Contact: francesco.emanuelli@iasma.it Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Background: The sweet, floral flavor typical of Muscat varieties (Muscats), due to high levels of monoterpenoids (geraniol, linalool and nerol), is highly distinct and has been greatly appreciated both in table grapes and in wine since ancient times. Muscat flavor determination in grape (Vitis vinifera L.) has up to now been studied by evaluating monoterpenoid levels through QTL analysis. These studies have revealed co-localization of 1-deoxy-D-xylulose 5-phosphate synthase (VvDXS) with the major QTL positioned on chromosome 5. Results: We resequenced VvDXS in an ad hoc association population of 148 grape varieties, which included muscat-flavored, aromatic and neutral accessions as well as muscat-like aromatic mutants and non-aromatic offsprings of Muscats. Gene nucleotide diversity and intragenic linkage disequilibrium (LD) were evaluated. Structured association analysis revealed three SNPs in moderate LD to be significantly associated with muscat-flavored varieties. We identified a putative causal SNP responsible for a predicted non-neutral substitution and we discuss its possible implications for flavor metabolism. Network analysis revealed a major star-shaped cluster of reconstructed haplotypes unique to muscat-flavored varieties. Moreover, muscat-like aromatic mutants displayed unique non-synonymous mutations near the mutated site of Muscat genotypes. Conclusions: This study is a crucial step forward in understanding the genetic regulation of muscat flavor in grapevine and it also sheds light on the domestication history of Muscats. VvDXS appears to be a possible human-selected locus in grapevine domestication and post-domestication. The putative causal SNP identified in Muscat varieties as well as the unique mutations identifying the muscat-like aromatic mutants under study may be immediately applied in marker-assisted breeding programs aimed at enhancing fragrance and aroma complexity respectively in table grape and wine cultivars

Published
2010

37. Developmental, molecular and genetic studies on grapevine response to temperature open breeding strategies for adaptation to warming

Author

Laurent Torregrosa, Antoine Bigard, Agnes Doligez, David Lecourieux, Markus Rienth, Nathalie Luchaire, Philippe Pieri, Ratthaphon Chatbanyong, Rezth Shahood, Marc Farnos, Catherine Roux, Angélique Adiveze, Jérémie Pillet, Yannick Sire, Emmanuelle Zumstein, Mélanie Veyret, Loic Le Cunff, Fatma Lecourieux, Nicolas Saurin, Bertrand Muller, Hernán Ojeda, Cléa Houel, Jean-Pierre Péros, Patrice This, Anne Pellegrino, and Charles Romieu

Subjects
global warming, temperature, grapevine, biology, adaptation, genetic improvement, Agriculture, Botany, QK1-989
Abstract

Aim: In the long term, genetic improvement is one of the major strategies to support sustainable wine production in a changing climate. Over the past 5 years, we have developed an interdisciplinary research program that aimed to: i) characterize the impact of temperature increase sensed by the entire plant or individual bunches on the development and functioning of the plant, ii) identify the physiological and molecular mechanisms regulating the response of vegetative and reproductive development to heat stress and iii) develop tools to map quantitative trait loci (QTLs) of plant and berry development in duly controlled, stable, and contrasting environmental conditions. Methods and results: Performing high-throughput genomic analyses combined with the use of innovative experimental designs (fruiting cuttings, microvines, single berry sampling) was critical to decipher the ecophysiological and molecular mechanisms involved in the vine response to high temperature. Conclusion: Warming promotes vegetative growth and hampers plant carbon balance, disturbing flower set and young berry development. High temperatures modify primary and secondary fruit metabolisms, desynchronizing sugar and organic acid metabolisms and delaying sugar and polyphenol accumulation during ripening. The study of day and night transcriptomic and proteomic signatures associated with heat highlighted key players of the response to temperature in the fruit. Significance and impact of the study: Capitalizing on this knowledge, a new program is being proposed for the selection of cultivars limiting the accumulation of sugars in the berry while maintaining other qualitative compounds.

Published
2017
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38. Focal Conic Stacking in Smectic A Liquid Crystals: Smectic Flower and Apollonius Tiling

Author

Malika Belloul, Guillaume Foyart, Loic Le Cunff, and Claire Meyer

Subjects
Defects, Focal conic domains, Liquid crystals, Smectic A, Apollonius tiling, Dupin cyclides, Technology, Electrical engineering. Electronics. Nuclear engineering, TK1-9971, Engineering (General). Civil engineering (General), TA1-2040, Microscopy, QH201-278.5, Descriptive and experimental mechanics, QC120-168.85
Abstract

We investigate two different textures of smectic A liquid crystals. These textures are particularly symmetric when they are observed at crossed polars optical microscopy. For both textures, a model has been made in order to examine the link between the defective macroscopic texture and the microscopic disposition of the layers. We present in particular in the case of some hexagonal tiling of circles (similar to the Apollonius tiling) some numeric simulation in order to visualize the smectic layers. We discuss of the nature of the smectic layers, which permit to assure their continuity from one focal conic domain to another adjacent one.

Published
2009
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39. Cultivar diversity of grape polyphenol composition and changes in response to drought investigated by LC-MS based metabolomics

Author

Veronique Cheynier, Lucie Pinasseau, Anna Vallverdu Queralt, Arnaud Verbaere, Maryline Roques, Emmanuelle Meudec, Loïc Le Cunff, Jean-Pierre Peros, Agnes Ageorges, Nicolas Sommerer, Jean Claude Boulet, Nancy Terrier, Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), University of Barcelona, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut Français de la Vigne et du Vin (IFV), European Project: 311775,EC:FP7:KBBE,FP7-KBBE-2012-6-singlestage,INNOVINE(2013), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, stress abiotique, Vegetal Biology, proanthocyanidine, composé phénolique, Agricultural sciences, chromatographie en phase liquide, stress biotique, oenologie, spectrométrie de masse, vin, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, stress hydrique, Biologie végétale, Sciences agricoles, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

40. ZnO as an effective fluorescence sensor for nitroaromatic derivatives

Author

Roy Aad, Vesna Simic, Loïc Le Cunff, Corinne Sartel, Vincent Sallet, Alain Lusson, Christophe Couteau, Gilles Lerondel, Laboratoire de Nanotechnologie et d'Instrumentation Optique (LNIO), Institut Charles Delaunay (ICD), Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Capteurs et Architectures Electroniques (LCAE), Département Métrologie Instrumentation & Information (DM2I), Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Groupe d'Etude de la Matière Condensée (GEMAC), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

41. SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects

Author

Alexis Dereeper, Jean-Pierre Péros, Manuel Ruiz, Patrice This, Agnès Doligez, Stéphane Nicolas, Roberto Bacilieri, Loïc Le Cunff, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), and Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Polymorphisme génétique, 01 natural sciences, Biochemistry, F30 - Génétique et amélioration des plantes, INDEL Mutation, Structural Biology, Vitis, lcsh:QH301-705.5, Phylogeny, Sanger sequencing, Genetics, 0303 health sciences, Applied Mathematics, Chromosome Mapping, SNP genotyping, Computer Science Applications, C30 - Documentation et information, symbols, Bio-informatique, lcsh:R858-859.7, génotype, Banque de données, Bioinformatics, conduite de la plante, logiciel, Context (language use), Single-nucleotide polymorphism, Computational biology, Biology, lcsh:Computer applications to medicine. Medical informatics, Polymorphism, Single Nucleotide, 03 medical and health sciences, symbols.namesake, vitis vinifera, Bioinformatique, Genotyping, Molecular Biology, 030304 developmental biology, diversité, Génie génétique, Genetic diversity, Internet, Base Sequence, génome, Computational Biology, Missing data, ComputingMethodologies_PATTERNRECOGNITION, lcsh:Biology (General), U30 - Méthodes de recherche, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], vigne, Sequence Alignment, Software, 010606 plant biology & botany, Reference genome
Abstract

Background High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. Results In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates: 1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D). Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices. 2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats. Conclusions Our experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies. SNiPlay is available at: http://sniplay.cirad.fr/.

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