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Brault C, Segura V, Roques M, Lamblin P, Bouckenooghe V, Pouzalgues N, Cunty C, Breil M, Frouin M, Garcin L, Camps L, Ducasse MA, Romieu C, Masson G, Julliard S, Flutre T, Le Cunff L. Enhancing grapevine breeding efficiency through genomic prediction and selection index. G3 (Bethesda) 2024; 14:jkae038. [PMID: 38401528 PMCID: PMC10989862 DOI: 10.1093/g3journal/jkae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/09/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Grapevine (Vitis vinifera) breeding reaches a critical point. New cultivars are released every year with resistance to powdery and downy mildews. However, the traditional process remains time-consuming, taking 20-25 years, and demands the evaluation of new traits to enhance grapevine adaptation to climate change. Until now, the selection process has relied on phenotypic data and a limited number of molecular markers for simple genetic traits such as resistance to pathogens, without a clearly defined ideotype, and was carried out on a large scale. To accelerate the breeding process and address these challenges, we investigated the use of genomic prediction, a methodology using molecular markers to predict genotypic values. In our study, we focused on 2 existing grapevine breeding programs: Rosé wine and Cognac production. In these programs, several families were created through crosses of emblematic and interspecific resistant varieties to powdery and downy mildews. Thirty traits were evaluated for each program, using 2 genomic prediction methods: Genomic Best Linear Unbiased Predictor and Least Absolute Shrinkage Selection Operator. The results revealed substantial variability in predictive abilities across traits, ranging from 0 to 0.9. These discrepancies could be attributed to factors such as trait heritability and trait characteristics. Moreover, we explored the potential of across-population genomic prediction by leveraging other grapevine populations as training sets. Integrating genomic prediction allowed us to identify superior individuals for each program, using multivariate selection index method. The ideotype for each breeding program was defined collaboratively with representatives from the wine-growing sector.
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Affiliation(s)
- Charlotte Brault
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Vincent Segura
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier 34398, France
| | - Maryline Roques
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Pauline Lamblin
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Virginie Bouckenooghe
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | | | - Constance Cunty
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Centre du Rosé, Vidauban 83550, France
| | - Matthieu Breil
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Marina Frouin
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Léa Garcin
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Louise Camps
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Marie-Agnès Ducasse
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
| | - Charles Romieu
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier 34398, France
| | - Gilles Masson
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
- Centre du Rosé, Vidauban 83550, France
| | - Sébastien Julliard
- Conservatoire du Vignoble Charentais, Institut de Formation de Richemont, Cherves-Richemont 16370, France
| | - Timothée Flutre
- INRAE, CNRS, AgroParisTech, Université Paris-Saclay, GQE—Le Moulon, Gif-sur-Yvette 91190, France
| | - Loïc Le Cunff
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, Montpellier 34398, France
- Institut Français de la vigne et du vin, Pôle National Matériel Végétal, Le Grau du Roi 30240, France
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2
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Coupel-Ledru A, Westgeest AJ, Albasha R, Millan M, Pallas B, Doligez A, Flutre T, Segura V, This P, Torregrosa L, Simonneau T, Pantin F. Clusters of grapevine genes for a burning world. New Phytol 2024; 242:10-18. [PMID: 38320579 DOI: 10.1111/nph.19540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024]
Affiliation(s)
| | | | - Rami Albasha
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- ITK, 45 Allée Yves Stourdze, F-34830, Clapiers, France
| | - Mathilde Millan
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Benoît Pallas
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Agnès Doligez
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398, Montpellier, France
| | - Timothée Flutre
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398, Montpellier, France
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Vincent Segura
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398, Montpellier, France
| | - Patrice This
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398, Montpellier, France
| | - Laurent Torregrosa
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398, Montpellier, France
| | | | - Florent Pantin
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000, Angers, France
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3
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Watson AE, Guitton B, Soriano A, Rivallan R, Vignes H, Farrera I, Huettel B, Arnaiz C, Falavigna VDS, Coupel-Ledru A, Segura V, Sarah G, Dufayard JF, Sidibe-Bocs S, Costes E, Andrés F. Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple. Front Plant Sci 2024; 15:1352757. [PMID: 38455730 PMCID: PMC10918860 DOI: 10.3389/fpls.2024.1352757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024]
Abstract
The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways.
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Affiliation(s)
- Amy E. Watson
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Baptiste Guitton
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Alexandre Soriano
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
| | - Ronan Rivallan
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Hélène Vignes
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Isabelle Farrera
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bruno Huettel
- Genome Centre, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Catalina Arnaiz
- Centro de Biotecnología y Genómica de Plantas, Instituto de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Aude Coupel-Ledru
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Vincent Segura
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gautier Sarah
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-François Dufayard
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
| | - Stéphanie Sidibe-Bocs
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
| | - Evelyne Costes
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Fernando Andrés
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Rogier O, Chateigner A, Lesage-Descauses MC, Mandin C, Brunaud V, Caius J, Soubigou-Taconnat L, Almeida-Falcon J, Bastien C, Benoit V, Bodineau G, Boizot N, Buret C, Charpentier JP, Déjardin A, Delaunay A, Fichot R, Laine Prade V, Laurans F, Le Jan I, Legac AL, Maury S, Gebreselassie MN, Poursat P, Ridel C, Sanchez L, Jorge V, Segura V. RNAseq based variant dataset in a black poplar association panel. BMC Res Notes 2023; 16:248. [PMID: 37784104 PMCID: PMC10546633 DOI: 10.1186/s13104-023-06521-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
OBJECTIVE Black poplar (Populus nigra L.) is a species native to Eurasia with a wide distribution area. It is an ecologically important species from riparian ecosystems, that is used as a parent of interspecific (P. deltoides x P. nigra) cultivated poplar hybrids. Variant detection from transcriptomics sequences of 241 P. nigra individuals, sampled in natural populations from 11 river catchments (in four European countries) is described here. These data provide new valuable resources for population structure analysis, population genomics and genome-wide association studies. DATA DESCRIPTION We generated transcriptomics data from a mixture of young differentiating xylem and cambium tissues of 480 Populus nigra trees sampled in a common garden experiment located at Orléans (France), corresponding to 241 genotypes (2 clonal replicates per genotype, at maximum) by using RNAseq technology. We launched on the resulting sequences an in-silico pipeline that allowed us to obtain 878,957 biallelic polymorphisms without missing data. More than 99% of these positions are annotated and 98.8% are located on the 19 chromosomes of the P. trichocarpa reference genome. The raw RNAseq sequences are available at the NCBI Sequence Read Archive SPR188754 and the variant dataset at the Recherche Data Gouv repository under https://doi.org/10.15454/8DQXK5 .
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Affiliation(s)
| | | | | | | | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - José Caius
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Groupe d’Étude et de Contrôle des Variétés et des Semences (GEVES), Station Nationale d’Essais de Semences (SNES), 49071 Beaucouzé, France
| | | | | | | | | | | | | | | | | | - Alain Delaunay
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, 45067 Orléans, France
| | - Régis Fichot
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, 45067 Orléans, France
| | | | | | - Isabelle Le Jan
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, 45067 Orléans, France
| | - Anne-Laure Legac
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, 45067 Orléans, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, 45067 Orléans, France
| | | | | | | | | | | | - Vincent Segura
- INRAE, ONF, BioForA, 45075 Orléans, France
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro Montpellier, Univ Montpellier, 34398 Montpellier, France
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5
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Blois L, de Miguel M, Bert P, Girollet N, Ollat N, Rubio B, Segura V, Voss‐Fels KP, Schmid J, Marguerit E. Genetic structure and first genome-wide insights into the adaptation of a wild relative of grapevine, Vitis berlandieri. Evol Appl 2023; 16:1184-1200. [PMID: 37360024 PMCID: PMC10286229 DOI: 10.1111/eva.13566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome-environment association analysis (GEA). De novo long-read whole-genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.
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Affiliation(s)
- Louis Blois
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
- Department of Grapevine BreedingGeisenheim UniversityGeisenheimGermany
| | - Marina de Miguel
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Pierre‐François Bert
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Nabil Girollet
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Nathalie Ollat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Bernadette Rubio
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
| | - Vincent Segura
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Kai P. Voss‐Fels
- Department of Grapevine BreedingGeisenheim UniversityGeisenheimGermany
| | - Joachim Schmid
- Department of Grapevine BreedingGeisenheim UniversityGeisenheimGermany
| | - Elisa Marguerit
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVVVillenave d'OrnonFrance
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Barotto AJ, Martínez-Meier A, Segura V, Monteoliva S, Charpentier JP, Gyenge J, Sergent AS, Millier F, Rozenberg P, Fernández ME. Use of near-infrared spectroscopy to estimate physical, anatomical and hydraulic properties of Eucalyptus wood. Tree Physiol 2023; 43:501-514. [PMID: 36383394 DOI: 10.1093/treephys/tpac132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/26/2022] [Accepted: 11/11/2022] [Indexed: 05/03/2023]
Abstract
Tree breeding programs and wood industries require simple, time- and cost-effective techniques to process large volumes of samples. In recent decades, near-infrared spectroscopy (NIRS) has been acknowledged as one of the most powerful techniques for wood analysis, making it the most used tool for high-throughput phenotyping. Previous studies have shown that a significant number of anatomical, physical, chemical and mechanical wood properties can be estimated through NIRS, both for angiosperm and gymnosperm species. However, the ability of this technique to predict functional traits related to drought resistance has been poorly explored, especially in angiosperm species. This is particularly relevant since determining xylem hydraulic properties by conventional techniques is complex and time-consuming, clearly limiting its use in studies and applications that demand large amounts of samples. In this study, we measured several wood anatomical and hydraulic traits and collected NIR spectra in branches of two Eucalyptus L'Hér species. We developed NIRS calibration models and discussed their ability to accurately predict the studied traits. The models generated allowed us to adequately calibrate the reference traits, with high R2 (≥0.75) for traits such as P12, P88, the slope of the vulnerability curves to xylem embolism or the fiber wall fraction, and with lower R2 (0.39-0.52) for P50, maximum hydraulic conductivity or frequency of ray parenchyma. We found that certain wavenumbers improve models' calibration, with those in the range of 4000-5500 cm-1 predicting the highest number of both anatomical and functional traits. We concluded that the use of NIRS allows calibrating models with potential predictive value not only for wood structural and chemical variables but also for anatomical and functional traits related to drought resistance in wood types with complex structure as eucalypts. These results are promising in light of the required knowledge about species and genotypes adaptability to global climatic change.
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Affiliation(s)
- Antonio José Barotto
- Cátedra de Dendrología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, CC 31 (1900) La Plata, Argentina
| | - Alejandro Martínez-Meier
- INTA EEA Bariloche, Grupo de Ecología Forestal, UEDD IFAB INTA-CONICET - Laboratorio de Ecología, Ecofisiología y Madera (LEEMA), Modesta Victoria 4450 (8400), Río Negro, Argentina
- Laboratorio Internacional Asociado LIA-Forestia (INTA - INRAE - UNAH)
| | - Vincent Segura
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | | | - Jean-Paul Charpentier
- UMR 0588 BioForA, INRAE, ONF, Orléans, France, 2163 Avenue de la Pomme de Pin, CS 40001 Ardon, 45075 Orléans Cedex 2, France
| | - Javier Gyenge
- Laboratorio Internacional Asociado LIA-Forestia (INTA - INRAE - UNAH)
- Grupo Forestal, UEDD IPADS INTA-CONICET-Oficina Tandil, Rodríguez 370 (7000), Tandil, Argentina
| | - Anne Sophie Sergent
- Laboratorio Internacional Asociado LIA-Forestia (INTA - INRAE - UNAH)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina UEDD IFAB INTA-CONICET - Laboratorio de Ecología, Ecofisiología y Madera (LEEMA), Modesta Victoria 4450 (8400), RíoNegro, Argentina
| | - Frédéric Millier
- UMR 0588 BioForA, INRAE, ONF, Orléans, France, 2163 Avenue de la Pomme de Pin, CS 40001 Ardon, 45075 Orléans Cedex 2, France
| | - Philippe Rozenberg
- Laboratorio Internacional Asociado LIA-Forestia (INTA - INRAE - UNAH)
- UMR 0588 BioForA, INRAE, ONF, Orléans, France, 2163 Avenue de la Pomme de Pin, CS 40001 Ardon, 45075 Orléans Cedex 2, France
| | - María Elena Fernández
- Laboratorio Internacional Asociado LIA-Forestia (INTA - INRAE - UNAH)
- Grupo Forestal, UEDD IPADS INTA-CONICET-Oficina Tandil, Rodríguez 370 (7000), Tandil, Argentina
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7
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Lutz V, Chidiak M, Frouin R, Negri R, Dogliotti AI, Santamaria-Del-Angel E, Berghoff CF, Rojas J, Filipello C, Astor Y, Segura V, Gonzalez-Silvera A, Escudero L, Ledesma J, Ueyoshi K, Silva RI, Ruiz MG, Cozzolino E, Allega L, Tan J, Kampel M. Regulation of CO 2 by the sea in areas around Latin America in a context of climate change. Environ Monit Assess 2023; 195:417. [PMID: 36807829 DOI: 10.1007/s10661-023-10997-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Anthropogenic activities are increasing the atmospheric carbon dioxide (CO2); around a third of the CO2 emitted by these activities has been taken up by the ocean. Nevertheless, this marine ecosystem service of regulation remains largely invisible to society, and not enough is known about regional differences and trends in sea-air CO2 fluxes (FCO2), especially in the Southern Hemisphere. The objectives of this work were as follows: first to put values of FCO2 integrated over the exclusive economic zones (EEZ) of five Latin-American countries (Argentina, Brazil, Mexico, Peru, and Venezuela) into perspective regarding total country-level greenhouse gases (GHG) emissions. Second, to assess the variability of two main biological factors affecting FCO2 at marine ecological time series (METS) in these areas. FCO2 over the EEZs were estimated using the NEMO model, and GHG emissions were taken from reports to the UN Framework Convention on Climate Change. For each METS, the variability in phytoplankton biomass (indexed by chlorophyll-a concentration, Chla) and abundance of different cell sizes (phy-size) were analyzed at two time periods (2000-2015 and 2007-2015). Estimates of FCO2 at the analyzed EEZs showed high variability among each other and non-negligible values in the context of greenhouse gas emissions. The trends observed at the METS indicated, in some cases, an increase in Chla (e.g., EPEA-Argentina) and a decrease in others (e.g., IMARPE-Peru). Evidence of increasing populations of small size-phytoplankton was observed (e.g., EPEA-Argentina, Ensenada-Mexico), which would affect the carbon export to the deep ocean. These results highlight the relevance of ocean health and its ecosystem service of regulation when discussing carbon net emissions and budgets.
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Affiliation(s)
- V Lutz
- CONICET-INIDEP, 7600, Mar del Plata, Argentina.
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina.
| | - M Chidiak
- Facultad de Ciencias Económicas, Instituto Interdisciplinario de Economía Política, Universidad de Buenos Aires, C1120AAQ, Buenos Aires, Argentina
| | - R Frouin
- Scripps Institution of Oceanography, University of California San Diego, 8810 Shellback Way, La Jolla, San Diego, CA, 92037, USA
| | - R Negri
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina
| | - A I Dogliotti
- Instituto de Astronomía Y Física del Espacio (IAFE), Pabellón IAFE, CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires C1428ZAA, Buenos Aires, Argentina
- Instituto Franco-Argentino Para El Estudio del Clima Y Sus Impactos (UMI-IFAECI, CNRSCONICET-UBA), C1428EGA, Buenos Aires, Argentina
| | - E Santamaria-Del-Angel
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860, Ensenada, México
| | - C F Berghoff
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina
| | - J Rojas
- Fundación La Salle de Ciencias Naturales Campus Margarita (EDIMAR), Isla Margarita, Venezuela
| | - C Filipello
- Facultad de Ciencias Económicas, Instituto Interdisciplinario de Economía Política, Universidad de Buenos Aires, C1120AAQ, Buenos Aires, Argentina
| | - Y Astor
- Fundación La Salle de Ciencias Naturales Campus Margarita (EDIMAR), Isla Margarita, Venezuela
| | - V Segura
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina
| | - A Gonzalez-Silvera
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860, Ensenada, México
| | - L Escudero
- Instituto del Mar del Perú, 07021, Callao, Perú
| | - J Ledesma
- Instituto del Mar del Perú, 07021, Callao, Perú
| | - K Ueyoshi
- Scripps Institution of Oceanography, University of California San Diego, 8810 Shellback Way, La Jolla, San Diego, CA, 92037, USA
| | - R I Silva
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina
| | - M G Ruiz
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina
| | - E Cozzolino
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina
| | - L Allega
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), 7600, Mar del Plata, Argentina
| | - J Tan
- Scripps Institution of Oceanography, University of California San Diego, 8810 Shellback Way, La Jolla, San Diego, CA, 92037, USA
| | - M Kampel
- Instituto Nacional de Pesquisas Espaciais, Sao Jose Dos Campos, 12227-010, Brazil
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8
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Brault C, Lazerges J, Doligez A, Thomas M, Ecarnot M, Roumet P, Bertrand Y, Berger G, Pons T, François P, Le Cunff L, This P, Segura V. Interest of phenomic prediction as an alternative to genomic prediction in grapevine. Plant Methods 2022; 18:108. [PMID: 36064570 PMCID: PMC9442960 DOI: 10.1186/s13007-022-00940-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
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.
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Affiliation(s)
- Charlotte Brault
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
- Institut Français de la vigne et du vin, 34398, Montpellier, France
| | - Juliette Lazerges
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Agnès Doligez
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Miguel Thomas
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
| | - Pierre Roumet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
| | - Yves Bertrand
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Gilles Berger
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Thierry Pons
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Pierre François
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Loïc Le Cunff
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
- Institut Français de la vigne et du vin, 34398, Montpellier, France
| | - Patrice This
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France
| | - Vincent Segura
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier, Montpellier, 34398, France.
- UMT Geno-Vigne®, IFV, INRAE, Institut Agro Montpellier, 34398, Montpellier, France.
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9
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Wade AR, Duruflé H, Sanchez L, Segura V. eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction. BMC Genomics 2022; 23:476. [PMID: 35764918 PMCID: PMC9238188 DOI: 10.1186/s12864-022-08690-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Multi-omics represent a promising link between phenotypes and genome variation. Few studies yet address their integration to understand genetic architecture and improve predictability. Results Our study used 241 poplar genotypes, phenotyped in two common gardens, with xylem and cambium RNA sequenced at one site, yielding large phenotypic, genomic (SNP), and transcriptomic datasets. Prediction models for each trait were built separately for SNPs and transcripts, and compared to a third model integrated by concatenation of both omics. The advantage of integration varied across traits and, to understand such differences, an eQTL analysis was performed to characterize the interplay between the genome and transcriptome and classify the predicting features into cis or trans relationships. A strong, significant negative correlation was found between the change in predictability and the change in predictor ranking for trans eQTLs for traits evaluated in the site of transcriptomic sampling. Conclusions Consequently, beneficial integration happens when the redundancy of predictors is decreased, likely leaving the stage to other less prominent but complementary predictors. An additional gene ontology (GO) enrichment analysis appeared to corroborate such statistical output. To our knowledge, this is a novel finding delineating a promising method to explore data integration. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08690-7.
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10
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Coupel‐Ledru A, Pallas B, Delalande M, Segura V, Guitton B, Muranty H, Durel C, Regnard J, Costes E. Tree architecture, light interception and water-use related traits are controlled by different genomic regions in an apple tree core collection. New Phytol 2022; 234:209-226. [PMID: 35023155 PMCID: PMC9305758 DOI: 10.1111/nph.17960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/19/2021] [Indexed: 05/17/2023]
Abstract
Tree architecture shows large genotypic variability, but how this affects water-deficit responses is poorly understood. To assess the possibility of reaching ideotypes with adequate combinations of architectural and functional traits in the face of climate change, we combined high-throughput field phenotyping and genome-wide association studies (GWAS) on an apple tree (Malus domestica) core-collection. We used terrestrial light detection and ranging (T-LiDAR) scanning and airborne multispectral and thermal imagery to monitor tree architecture, canopy shape, light interception, vegetation indices and transpiration on 241 apple cultivars submitted to progressive field soil drying. GWAS was performed with single nucleotide polymorphism (SNP)-by-SNP and multi-SNP methods. Large phenotypic and genetic variability was observed for all traits examined within the collection, especially canopy surface temperature in both well-watered and water deficit conditions, suggesting control of water loss was largely genotype-dependent. Robust genomic associations revealed independent genetic control for the architectural and functional traits. Screening associated genomic regions revealed candidate genes involved in relevant pathways for each trait. We show that multiple allelic combinations exist for all studied traits within this collection. This opens promising avenues to jointly optimize tree architecture, light interception and water use in breeding strategies. Genotypes carrying favourable alleles depending on environmental scenarios and production objectives could thus be targeted.
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Affiliation(s)
- Aude Coupel‐Ledru
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Benoît Pallas
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Magalie Delalande
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Vincent Segura
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Baptiste Guitton
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Hélène Muranty
- IRHSSFR QuaSaVUniversité d’Angers, Institut Agro, INRAE49000AngersFrance
| | - Charles‐Eric Durel
- IRHSSFR QuaSaVUniversité d’Angers, Institut Agro, INRAE49000AngersFrance
| | - Jean‐Luc Regnard
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
| | - Evelyne Costes
- AGAP InstitutUniv Montpellier, CIRAD, INRAE, Institut Agro34398MontpellierFrance
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11
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Brault C, Segura V, This P, Le Cunff L, Flutre T, François P, Pons T, Péros JP, Doligez A. Across-population genomic prediction in grapevine opens up promising prospects for breeding. Hortic Res 2022; 9:uhac041. [PMID: 35184162 PMCID: PMC9070645 DOI: 10.1093/hr/uhac041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/01/2022] [Indexed: 05/15/2023]
Abstract
Crop breeding involves two selection steps: choosing progenitors and selecting individuals within progenies. Genomic prediction, based on genome-wide marker estimation of genetic values, could facilitate these steps. However, its potential usefulness in grapevine (Vitis vinifera L.) 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.
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Affiliation(s)
- Charlotte Brault
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- Institut Français de la Vigne et du Vin, F-34398 Montpellier, France
| | - Vincent Segura
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Patrice This
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Loïc Le Cunff
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- Institut Français de la Vigne et du Vin, F-34398 Montpellier, France
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190, Gif-sur-Yvette, France
| | - Pierre François
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Thierry Pons
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Jean-Pierre Péros
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Agnès Doligez
- UMT Geno-Vigne®, IFV-INRAE-Institut Agro, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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12
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Persoons A, Maupetit A, Louet C, Andrieux A, Lipzen A, Barry KW, Na H, Adam C, Grigoriev IV, Segura V, Duplessis S, Frey P, Halkett F, De Mita S. Genomic signatures of a major adaptive event in the pathogenic fungus Melampsora larici-populina. Genome Biol Evol 2021; 14:6468622. [PMID: 34919678 PMCID: PMC8755504 DOI: 10.1093/gbe/evab279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based on 76 virulent and avirulent isolates framing narrowly the estimated date of the adaptive event, we examined the molecular signatures of selection. Using an array of genome scan methods based on different features of nucleotide diversity, we detected a single locus exhibiting a consistent pattern suggestive of a selective sweep in virulent individuals (excess of differentiation between virulent and avirulent samples, linkage disequilibrium, genotype–phenotype statistical association, and long-range haplotypes). Our study pinpoints a single gene and further a single amino acid replacement which may have allowed the adaptive event. Although our samples are nearly contemporary to the selective sweep, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus, which can be explained by a soft selective sweep (where selection acts on standing variation) and by the impact of recombination in mitigating the impact of selection. Therefore, it seems that properties of the life cycle of M. larici-populina, which entails both high genetic diversity and outbreeding, has facilitated its adaptation.
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Affiliation(s)
| | - Agathe Maupetit
- Université de Lorraine,INRAE, IAM, Nancy, France.,Physiology and Biotechnology of Algae Laboratory,IFREMER, Nantes, France
| | | | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kerrie W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Catherine Adam
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Vincent Segura
- BioForA,INRAE, ONF, Orléans, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | | | - Pascal Frey
- Université de Lorraine,INRAE, IAM, Nancy, France
| | | | - Stéphane De Mita
- Université de Lorraine,INRAE, IAM, Nancy, France.,PHIM, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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13
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Sow MD, Le Gac AL, Fichot R, Lanciano S, Delaunay A, Le Jan I, Lesage-Descauses MC, Citerne S, Caius J, Brunaud V, Soubigou-Taconnat L, Cochard H, Segura V, Chaparro C, Grunau C, Daviaud C, Tost J, Brignolas F, Strauss SH, Mirouze M, Maury S. RNAi suppression of DNA methylation affects the drought stress response and genome integrity in transgenic poplar. New Phytol 2021; 232:80-97. [PMID: 34128549 DOI: 10.1111/nph.17555] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/08/2021] [Indexed: 05/27/2023]
Abstract
Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via downregulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula × Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit. We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.
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Affiliation(s)
- Mamadou D Sow
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Anne-Laure Le Gac
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Sophie Lanciano
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Isabelle Le Jan
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | | | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Jose Caius
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Hervé Cochard
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, 63000, France
| | - Vincent Segura
- BioForA, INRAE, ONF, UMR 0588, Orléans, 45075, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Montpellier SupAgro, UMR 1334, Montpellier, F-34398, France
| | | | - Christoph Grunau
- UMR 5244, IHPE, Université de Perpignan, Perpignan, 66100, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Franck Brignolas
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Marie Mirouze
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
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14
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Balcarcel AM, Sánchez-Villagra MR, Segura V, Evin A. Singular patterns of skull shape and brain size change in the domestication of South American camelids. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Patterns of selection in South American camelids (Lamini) and their unique demographic history establish the llama and alpaca as remarkable cases of domestication among large herd animals. Skull shape is implicated in many changes reported between wild and domestic taxa. We apply 3D geometric morphometric methods to describe skull shape, form, and size, differences among the four species of Lamini. In so doing, we test if domesticated Lamini exhibit changes similar to those in other domesticated groups: not only in the skull, but also in brain and body size. In contrast to other domesticated artiodactyls, very little change has occurred in domestic alpacas and llamas compared to their wild counterparts. Nevertheless, their differences are statistically significant and include a flatter cranium, inclined palate and increased airorhynchy in the domestics. Selection pressures that contrast with those on other herd animals, as well as recent population bottlenecks, likely have influenced the morphological patterns we note in Lamini. High-resolution 3D morphospace allows skull size, shape, and form (shape + size), to discriminate all four species, with form providing the greatest separation. These results help differentiate morphologically the Lamini, which in nature are distinguished mainly by body size, and provide an additional tool to archaeologists for distinction of wild and domestic remains. Most of our shape analyses suggest a marginally closer relationship between the alpaca and vicuña, to the exclusion of the guanaco, supporting the genetic relationships for this group. The expected brain size change between wild and domestic populations is lower than previously thought, with a 15.4% reduction in llama, and 6.8% reduction in alpaca. This is the lowest reduction in brain size thus far reported among domesticated Artiodactyla.
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Affiliation(s)
- A M Balcarcel
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Strasse, Zurich, Switzerland
| | - M R Sánchez-Villagra
- Palaeontological Institute and Museum, University of Zurich, Karl-Schmid-Strasse, Zurich, Switzerland
| | - V Segura
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas–Fundación Miguel Lillo, Miguel Lillo, San Miguel de Tucumán, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), AAH Buenos Aires, Argentina
| | - A Evin
- Institut des sciences de l’évolution, Université de Montpellier, CNRS, IRD, EPHE, Montpellier Cedex, France
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Abercromby Square, Liverpool, United Kingdom
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15
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Pégard M, Segura V, Muñoz F, Bastien C, Jorge V, Sanchez L. Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar. Front Plant Sci 2020; 11:581954. [PMID: 33193528 PMCID: PMC7655903 DOI: 10.3389/fpls.2020.581954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Forest trees like poplar are particular in many ways compared to other domesticated species. They have long juvenile phases, ongoing crop-wild gene flow, extensive outcrossing, and slow growth. All these particularities tend to make the conduction of breeding programs and evaluation stages costly both in time and resources. Perennials like trees are therefore good candidates for the implementation of genomic selection (GS) which is a good way to accelerate the breeding process, by unchaining selection from phenotypic evaluation without affecting precision. In this study, we tried to compare GS to pedigree-based traditional evaluation, and evaluated under which conditions genomic evaluation outperforms classical pedigree evaluation. Several conditions were evaluated as the constitution of the training population by cross-validation, the implementation of multi-trait, single trait, additive and non-additive models with different estimation methods (G-BLUP or weighted G-BLUP). Finally, the impact of the marker densification was tested through four marker density sets. The population under study corresponds to a pedigree of 24 parents and 1,011 offspring, structured into 35 full-sib families. Four evaluation batches were planted in the same location and seven traits were evaluated on 1 and 2 years old trees. The quality of prediction was reported by the accuracy, the Spearman rank correlation and prediction bias and tested with a cross-validation and an independent individual test set. Our results show that genomic evaluation performance could be comparable to the already well-optimized pedigree-based evaluation under certain conditions. Genomic evaluation appeared to be advantageous when using an independent test set and a set of less precise phenotypes. Genome-based methods showed advantages over pedigree counterparts when ranking candidates at the within-family levels, for most of the families. Our study also showed that looking at ranking criteria as Spearman rank correlation can reveal benefits to genomic selection hidden by biased predictions.
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Affiliation(s)
| | - Vincent Segura
- BioForA, INRA, ONF, Orléans, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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16
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Juan Ribelles A, Gargallo P, Ferriol C, Segura V, Yáñez Y, Juan B, Cañada AJ, Font de Mora J, Cañete A, Castel V. Distribution of segmental chromosomal alterations in neuroblastoma. Clin Transl Oncol 2020; 23:1096-1104. [PMID: 32948984 DOI: 10.1007/s12094-020-02497-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/05/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is a heterogeneous tumor with extremely diverse prognosis according to clinical and genetic factors such as specific combinations of chromosomal imbalances. METHODS Molecular karyotyping data from a national neuroblastic tumor database of 155 NB samples were analyzed and related to clinical data. RESULTS Segmental chromosomal alterations (SCA) were detected in 102 NB, whereas 45 only displayed numerical alterations. Incidence of SCA was higher in stage M (92%) and MYCN amplified (MNA) NB (96%). Presence of SCA was associated with older age, especially 1q gain and 3p deletion. 96% of the deaths were observed in the SCA group and 85% of the relapsed NB contained SCA. The alteration most commonly associated with a higher number of other segmental rearrangements was 11q deletion, followed by 4p deletion. Whole-chromosome 19 gain was associated with lower stages, absence of SCA and better outcome. CONCLUSIONS SCA are not randomly distributed and are concentrated on recurrent chromosomes. The most frequently affected chromosomes identify prognostic factors in specific risk groups. SCA are associated with older age and MNA. We have identified a small subset of patients with better outcome that share whole-chromosome 19 numeric gain, suggesting its use as a prognostic biomarker in NB.
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Affiliation(s)
- A Juan Ribelles
- Pediatric Oncology and Hematology Unit, Hospital U i P La Fe, Av. Fernando Abril Martorell, 106, Valencia, Spain.
| | - P Gargallo
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - C Ferriol
- Universitat de València, Valencia, Spain
| | - V Segura
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - Y Yáñez
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - B Juan
- Universitat de València, Valencia, Spain
| | - A J Cañada
- Biostatistics Department, Instituto de Investigación La Fe, Valencia, Spain
| | - J Font de Mora
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - A Cañete
- Pediatric Oncology and Hematology Unit, Hospital U i P La Fe, Av. Fernando Abril Martorell, 106, Valencia, Spain
| | - V Castel
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
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17
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Chateigner A, Lesage-Descauses MC, Rogier O, Jorge V, Leplé JC, Brunaud V, Roux CPL, Soubigou-Taconnat L, Martin-Magniette ML, Sanchez L, Segura V. Gene expression predictions and networks in natural populations supports the omnigenic theory. BMC Genomics 2020; 21:416. [PMID: 32571208 PMCID: PMC7310122 DOI: 10.1186/s12864-020-06809-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/08/2020] [Indexed: 02/03/2023] Open
Abstract
Background Recent literature on the differential role of genes within networks distinguishes core from peripheral genes. If previous works have shown contrasting features between them, whether such categorization matters for phenotype prediction remains to be studied. Results We measured 17 phenotypic traits for 241 cloned genotypes from a Populus nigra collection, covering growth, phenology, chemical and physical properties. We also sequenced RNA for each genotype and built co-expression networks to define core and peripheral genes. We found that cores were more differentiated between populations than peripherals while being less variable, suggesting that they have been constrained through potentially divergent selection. We also showed that while cores were overrepresented in a subset of genes statistically selected for their capacity to predict the phenotypes (by Boruta algorithm), they did not systematically predict better than peripherals or even random genes. Conclusion Our work is the first attempt to assess the importance of co-expression network connectivity in phenotype prediction. While highly connected core genes appear to be important, they do not bear enough information to systematically predict better quantitative traits than other gene sets.
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Affiliation(s)
| | | | | | | | | | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Sud, Université d'Evry, Université Paris-Saclay, Gif sur Yvette, France.,Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Diderot, Sorbonne Paris-Cité, Gif sur Yvette, France
| | - Christine Paysant-Le Roux
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Sud, Université d'Evry, Université Paris-Saclay, Gif sur Yvette, France.,Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Diderot, Sorbonne Paris-Cité, Gif sur Yvette, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Sud, Université d'Evry, Université Paris-Saclay, Gif sur Yvette, France.,Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Diderot, Sorbonne Paris-Cité, Gif sur Yvette, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Sud, Université d'Evry, Université Paris-Saclay, Gif sur Yvette, France.,Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Diderot, Sorbonne Paris-Cité, Gif sur Yvette, France.,MIA-Paris, AgroParisTech, INRAE, Paris, France
| | | | - Vincent Segura
- BioForA, INRAE, ONF, Orléans, France. .,AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France.
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18
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Gargallo P, Yáñez Y, Segura V, Juan A, Torres B, Balaguer J, Oltra S, Castel V, Cañete A. Li-Fraumeni syndrome heterogeneity. Clin Transl Oncol 2019; 22:978-988. [PMID: 31691207 DOI: 10.1007/s12094-019-02236-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/21/2019] [Indexed: 02/07/2023]
Abstract
Clinical variability is commonly seen in Li-Fraumeni syndrome. Phenotypic heterogeneity is present among different families affected by the same pathogenic variant in TP53 gene and among members of the same family. However, causes of this huge clinical spectrum have not been studied in depth. TP53 type mutation, polymorphic variants in TP53 gene or in TP53-related genes, copy number variations in particular regions, and/or epigenetic deregulation of TP53 expression might be responsible for clinical heterogeneity. In this review, recent advances in the understanding of genetic and epigenetic aspects influencing Li-Fraumeni phenotype are discussed.
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Affiliation(s)
- P Gargallo
- Pediatric Oncology, La Fe Hospital, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain.
| | - Y Yáñez
- Clinical and Translational Oncology Research Group, La Fe Hospital, Valencia, Spain
| | - V Segura
- Clinical and Translational Oncology Research Group, La Fe Hospital, Valencia, Spain
| | - A Juan
- Pediatric Oncology, La Fe Hospital, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - B Torres
- Pediatric Oncology, La Fe Hospital, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - J Balaguer
- Pediatric Oncology, La Fe Hospital, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - S Oltra
- Genetics Unit, La Fe Hospital, Valencia, Spain.,Genetics Department, Valencia University, Valencia, Spain
| | - V Castel
- Pediatric Oncology, La Fe Hospital, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - A Cañete
- Pediatric Oncology, La Fe Hospital, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain
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19
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Rogier O, Chateigner A, Amanzougarene S, Lesage-Descauses MC, Balzergue S, Brunaud V, Caius J, Soubigou-Taconnat L, Jorge V, Segura V. Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra. BMC Genomics 2018; 19:909. [PMID: 30541448 PMCID: PMC6291945 DOI: 10.1186/s12864-018-5239-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/09/2018] [Indexed: 12/30/2022] Open
Abstract
Backgroud Populus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Polymorphisms (SNPs) typically needed to carry out a genome scan, the present study aimed at evaluating RNA sequencing as a tool to discover and type SNPs in genes within natural populations of P. nigra. Results We have devised a bioinformatics pipeline to call and type SNPs from RNAseq reads and applied it to P. nigra transcriptomic data. The accuracy of the resulting RNAseq-based SNP calling and typing has been evaluated by (i) comparing their position and alleles to those previously reported in candidate genes, (ii) assessing their genotyping accuracy with respect to a previously available SNP chip and (iii) evaluating their inter-annual repeatability. We found that a combination of several callers yields a good compromise between the number of variants type and the accuracy of genotyping. We further used the resulting genotypic data to carry out basic genetic analyses whose results confirm the quality of the RNAseq-based SNP dataset. Conclusions We demonstrated the potential and accuracy of RNAseq as an efficient way to genotype SNPs in P. nigra. These results open prospects towards the use of this technology for quantitative and population genomics studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-5239-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Sandrine Balzergue
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France.,IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, Beaucouzé, 49071, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
| | - José Caius
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
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20
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Rincent R, Charpentier JP, Faivre-Rampant P, Paux E, Le Gouis J, Bastien C, Segura V. Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar. G3 (Bethesda) 2018; 8:3961-3972. [PMID: 30373914 PMCID: PMC6288839 DOI: 10.1534/g3.118.200760] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/20/2018] [Indexed: 11/29/2022]
Abstract
Genomic selection - the prediction of breeding values using DNA polymorphisms - is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown that other sources of molecular variations such as those resulting from transcripts or metabolites could be used to accurately predict complex traits. These endophenotypes have the advantage of capturing the expressed genotypes and consequently the complex regulatory networks that occur in the different layers between the genome and the phenotype. However, obtaining such omics data at very large scales, such as those typically experienced in breeding, remains challenging. As an alternative, we proposed using near-infrared spectroscopy (NIRS) as a high-throughput, low cost and non-destructive tool to indirectly capture endophenotypic variants and compute relationship matrices for predicting complex traits, and coined this new approach "phenomic selection" (PS). We tested PS on two species of economic interest (Triticum aestivum L. and Populus nigra L.) using NIRS on various tissues (grains, leaves, wood). We showed that one could reach predictions as accurate as with molecular markers, for developmental, tolerance and productivity traits, even in environments radically different from the one in which NIRS were collected. Our work constitutes a proof of concept and provides new perspectives for the breeding community, as PS is theoretically applicable to any organism at low cost and does not require any molecular information.
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Affiliation(s)
| | - Jean-Paul Charpentier
- BioForA, INRA, ONF, 45075 Orléans, France
- GenoBois analytical platform, INRA, 45075 Orléans, France
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21
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Perez Gracia J, Pajares M, Fusco J, Andueza M, Segura V, Mora M, Guruceaga E, Sanchez Bayona R, Gurpide A, Lopez-Picazo J, Gil-Bazo I, de Torres J, Zulueta J, Pio R, Melero I, Sanmamed M, Rodriguez-Ruiz M, Gonzalez Neira A, Montuenga L, Patiño-Garcia A. Characterization through whole exome sequencing of individuals presenting extreme phenotypes of high and low risk to develop tobacco-induced non-small lung cancer (NSCLC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy303.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Le Gac AL, Lafon-Placette C, Chauveau D, Segura V, Delaunay A, Fichot R, Marron N, Le Jan I, Berthelot A, Bodineau G, Bastien JC, Brignolas F, Maury S. Winter-dormant shoot apical meristem in poplar trees shows environmental epigenetic memory. J Exp Bot 2018; 69:4821-4837. [PMID: 30107545 PMCID: PMC6137975 DOI: 10.1093/jxb/ery271] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/02/2018] [Indexed: 05/04/2023]
Abstract
Trees have a long lifespan and must continually adapt to environmental pressures, notably in the context of climate change. Epigenetic mechanisms are doubtless involved in phenotypic plasticity and in stress memory; however, little evidence of the role of epigenetic processes is available for trees growing in fields. Here, we analyzed the possible involvement of epigenetic mechanisms in the winter-dormant shoot apical meristem of Populus × euramericana clones in memory of the growing conditions faced during the vegetative period. We aimed to estimate the range of genetic and environmentally induced variations in global DNA methylation and to evaluate their correlation with changes in biomass production, identify differentially methylated regions (DMRs), and characterize common DMRs between experiments. We showed that the variations in global DNA methylation between conditions were genotype dependent and correlated with biomass production capacity. Microarray chip analysis allowed detection of DMRs 6 months after the stressful summer period. The 161 DMRs identified as common to three independent experiments most notably targeted abiotic stress and developmental response genes. Results are consistent with a winter-dormant shoot apical meristem epigenetic memory of stressful environmental conditions that occurred during the preceding summer period. This memory may facilitate tree acclimation.
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Affiliation(s)
| | | | | | | | | | - Régis Fichot
- LBLGC, INRA, Université d’Orléans, Orléans, France
| | - Nicolas Marron
- Silva, INRA Grand Est, Nancy, AgroParisTech, Université de Lorraine, UMR, Nancy, France
| | | | - Alain Berthelot
- FCBA Délégation Territoriale Nord-Est, Charrey-Sur-Saône, France
| | | | | | | | - Stéphane Maury
- LBLGC, INRA, Université d’Orléans, Orléans, France
- Correspondence:
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23
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Gargallo P, Oltra JS, Yáñez Y, Segura V, Balaguer J, Cañete A. Retinoblastoma: towards an earlier diagnosis. ACTA ACUST UNITED AC 2018; 93:439-443. [PMID: 29929761 DOI: 10.1016/j.oftal.2018.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/26/2018] [Accepted: 05/09/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The number of enucleations and visual sequels due to retinoblastoma is high. The aim of this study was to evaluate the different diagnostic aspects and propose strategies that might improve the clinical management of this condition. METHOD A retrospective study was conducted on 38 patients with retinoblastoma studied genetically (29 unilateral, 9 bilateral). The evaluation included: age of onset, clinical signs, and time since onset, number of enucleations, time to diagnosis, and survival at 5 years. RESULTS Leukocoria was the main clinical sign (present in 90% of cases). The mean diagnostic delay was 3.2 months. Among the unilateral cases, the eyes were enucleated in 76%, and 55% in the bilateral forms. Only one death was found among the 25 patients followed-up for at least 5 years. CONCLUSIONS Retinoblastoma diagnostic and treatment strategies need to be updated. Good coordination between paediatricians and ophthalmologists is essential for this. Its management in reference centres, which have the necessary technology and experience, should contribute to increase the rate of organ preservation.
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Affiliation(s)
- P Gargallo
- Grupo de Investigación Clínica y Traslacional en Cáncer, Instituto de Investigación Sanitaria La Fe, Valencia, España.
| | - J S Oltra
- Servicio de Genética Médica, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Y Yáñez
- Grupo de Investigación Clínica y Traslacional en Cáncer, Instituto de Investigación Sanitaria La Fe, Valencia, España
| | - V Segura
- Grupo de Investigación Clínica y Traslacional en Cáncer, Instituto de Investigación Sanitaria La Fe, Valencia, España
| | - J Balaguer
- Oncología Pediátrica, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - A Cañete
- Oncología Pediátrica, Hospital Universitario y Politécnico La Fe, Valencia, España
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24
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Lafon-Placette C, Le Gac AL, Chauveau D, Segura V, Delaunay A, Lesage-Descauses MC, Hummel I, Cohen D, Jesson B, Le Thiec D, Bogeat-Triboulot MB, Brignolas F, Maury S. Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways. J Exp Bot 2018; 69:537-551. [PMID: 29211860 DOI: 10.1093/jxb/erx409] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/25/2017] [Indexed: 05/04/2023]
Abstract
The adaptive capacity of long-lived organisms such as trees to the predicted climate changes, including severe and successive drought episodes, will depend on the presence of genetic diversity and phenotypic plasticity. Here, the involvement of epigenetic mechanisms in phenotypic plasticity toward soil water availability was examined in Populus×euramericana. This work aimed at characterizing (i) the transcriptome plasticity, (ii) the genome-wide plasticity of DNA methylation, and (iii) the function of genes affected by a drought-rewatering cycle in the shoot apical meristem. Using microarray chips, differentially expressed genes (DEGs) and differentially methylated regions (DMRs) were identified for each water regime. The rewatering condition was associated with the highest variations of both gene expression and DNA methylation. Changes in methylation were observed particularly in the body of expressed genes and to a lesser extent in transposable elements. Together, DEGs and DMRs were significantly enriched in genes related to phytohormone metabolism or signaling pathways. Altogether, shoot apical meristem responses to changes in water availability involved coordinated variations in DNA methylation, as well as in gene expression, with a specific targeting of genes involved in hormone pathways, a factor that may enable phenotypic plasticity.
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Affiliation(s)
| | | | | | | | - Alain Delaunay
- LBLGC EA 1207, INRA, Université d'Orléans, USC 1328, France
| | | | - Irène Hummel
- EEF, INRA Grand-Est-Nancy, Université de Lorraine, UMR 1137, France
| | - David Cohen
- EEF, INRA Grand-Est-Nancy, Université de Lorraine, UMR 1137, France
| | | | - Didier Le Thiec
- EEF, INRA Grand-Est-Nancy, Université de Lorraine, UMR 1137, France
| | | | | | - Stéphane Maury
- LBLGC EA 1207, INRA, Université d'Orléans, USC 1328, France
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Bauchet G, Grenier S, Samson N, Segura V, Kende A, Beekwilder J, Cankar K, Gallois JL, Gricourt J, Bonnet J, Baxter C, Grivet L, Causse M. Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement. New Phytol 2017; 215:624-641. [PMID: 28585324 DOI: 10.1111/nph.14615] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/09/2017] [Indexed: 05/21/2023]
Abstract
Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite content and genetic inheritance of metabolites varied broadly, both within and between different genetic groups. Using genotype information gained from 10 000 single nucleotide polymorphism markers, we performed a metabolite genome-wide association mapping (GWAS) study. We identified 79 associations influencing 13 primary and 19 secondary metabolites with large effects at high resolution. Four genome regions were detected, highlighting clusters of associations controlling the variation of several metabolites. Local linkage disequilibrium analysis and allele mining identified possible candidate genes which may modulate the content of metabolites that are of significant importance for human diet and fruit consumption. We precisely characterized two associations involved in fruit acidity and phenylpropanoid volatile production. Taken together, this study reveals complex and distinct metabolite regulation in tomato subspecies and demonstrates that GWAS is a powerful tool for gene-metabolite annotation and identification, pathways elucidation, and further crop improvement.
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Affiliation(s)
- Guillaume Bauchet
- INRA, UR1052, GAFL, 67 Allée des Chênes Domaine Saint Maurice - CS60094, Montfavet Cedex, 84143, France
- Syngenta, 12 Chemin de l'Hobit, Saint Sauveur, 31790, France
| | | | - Nicolas Samson
- Syngenta, 12 Chemin de l'Hobit, Saint Sauveur, 31790, France
| | | | - Aniko Kende
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Jules Beekwilder
- Plant Research International, 6700 AA, Wageningen, the Netherlands
| | - Katarina Cankar
- Plant Research International, 6700 AA, Wageningen, the Netherlands
| | - Jean-Luc Gallois
- INRA, UR1052, GAFL, 67 Allée des Chênes Domaine Saint Maurice - CS60094, Montfavet Cedex, 84143, France
| | - Justine Gricourt
- INRA, UR1052, GAFL, 67 Allée des Chênes Domaine Saint Maurice - CS60094, Montfavet Cedex, 84143, France
| | - Julien Bonnet
- Syngenta, 12 Chemin de l'Hobit, Saint Sauveur, 31790, France
| | - Charles Baxter
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Laurent Grivet
- Syngenta, 12 Chemin de l'Hobit, Saint Sauveur, 31790, France
| | - Mathilde Causse
- INRA, UR1052, GAFL, 67 Allée des Chênes Domaine Saint Maurice - CS60094, Montfavet Cedex, 84143, France
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26
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Talamillo A, Grande L, Ruiz-Ontañon P, Velasquez C, Mollinedo P, Torices S, Sanchez-Gomez P, Aznar A, Esparis-Ogando A, Lopez-Lopez C, Lafita C, Berciano MT, Montero JA, Vazquez-Barquero A, Segura V, Villagra NT, Pandiella A, Lafarga M, Leon J, Martinez-Climent JA, Sanz-Moreno V, Fernandez-Luna JL. ODZ1 allows glioblastoma to sustain invasiveness through a Myc-dependent transcriptional upregulation of RhoA. Oncogene 2017; 36:1733-1744. [PMID: 27641332 DOI: 10.1038/onc.2016.341] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 08/01/2016] [Accepted: 08/10/2016] [Indexed: 02/06/2023]
Abstract
Long-term survival remains low for most patients with glioblastoma (GBM), which reveals the need for markers of disease outcome and novel therapeutic targets. We describe that ODZ1 (also known as TENM1), a type II transmembrane protein involved in fetal brain development, plays a crucial role in the invasion of GBM cells. Differentiation of glioblastoma stem-like cells drives the nuclear translocation of an intracellular fragment of ODZ1 through proteolytic cleavage by signal peptide peptidase-like 2a. The intracellular fragment of ODZ1 promotes cytoskeletal remodelling of GBM cells and invasion of the surrounding environment both in vitro and in vivo. Absence of ODZ1 by gene deletion or downregulation of ODZ1 by small interfering RNAs drastically reduces the invasive capacity of GBM cells. This activity is mediated by an ODZ1-triggered transcriptional pathway, through the E-box binding Myc protein, that promotes the expression and activation of Ras homolog family member A (RhoA) and subsequent activation of Rho-associated, coiled-coil containing protein kinase (ROCK). Overexpression of ODZ1 in GBM cells reduced survival of xenografted mice. Consistently, analysis of 122 GBM tumour samples revealed that the number of ODZ1-positive cells inversely correlated with overall and progression-free survival. Our findings establish a novel marker of invading GBM cells and consequently a potential marker of disease progression and a therapeutic target in GBM.
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Affiliation(s)
- A Talamillo
- Unidad de Genética, Hospital Valdecilla-IDIVAL, Santander, Spain
| | - L Grande
- Unidad de Genética, Hospital Valdecilla-IDIVAL, Santander, Spain
| | - P Ruiz-Ontañon
- Unidad de Genética, Hospital Valdecilla-IDIVAL, Santander, Spain
| | - C Velasquez
- Servicio de Neurocirugía, Hospital Valdecilla-IDIVAL, Santander, Spain
| | - P Mollinedo
- Unidad de Genética, Hospital Valdecilla-IDIVAL, Santander, Spain
| | - S Torices
- Unidad de Genética, Hospital Valdecilla-IDIVAL, Santander, Spain
| | - P Sanchez-Gomez
- Unidad de Neuro-Oncología, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - A Aznar
- Centro para la Investigación Médica Aplicada (CIMA), Pamplona, Spain
| | - A Esparis-Ogando
- Centro de Investigación del Cáncer (CSIC-USAL), Salamanca, Spain
| | - C Lopez-Lopez
- Servicio de Oncología Médica, Hospital Valdecilla-IDIVAL, Santander, Spain
| | - C Lafita
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
| | - M T Berciano
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, Spain
| | - J A Montero
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, Spain
| | | | - V Segura
- Centro para la Investigación Médica Aplicada (CIMA), Pamplona, Spain
| | - N T Villagra
- Servicio de Anatomía Patológica, Hospital Valdecilla and Instituto de Investigación Valdecilla (IDIVAL), Santander, Spain
| | - A Pandiella
- Centro de Investigación del Cáncer (CSIC-USAL), Salamanca, Spain
| | - M Lafarga
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, Santander, Spain
| | - J Leon
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
| | | | - V Sanz-Moreno
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, UK
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Albert E, Segura V, Gricourt J, Bonnefoi J, Derivot L, Causse M. Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits. J Exp Bot 2016; 67:6413-6430. [PMID: 27856709 PMCID: PMC5181584 DOI: 10.1093/jxb/erw411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Vincent Segura
- INRA, UR0588, Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, Centre de Recherche Val de Loire, CS 40001, Orléans, 45075, France
| | - Justine Gricourt
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | | | | | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
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28
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Nuñez M, Nuñez E, Lozano L, Segur J, Montañana J, Segura V, Salo S, Alemany X, Sastre S. THU0624 Sleep Quality in Patients with Severe Knee Osteroarthritis. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.2156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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29
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Nicolás D, Esteve A, Cuadros A, Campbell CNJ, Tural C, Podzamczer D, Murillas J, Homar F, Segura F, Force L, Vilaró J, Masabeu À, Garcia I, Mercadal J, Montoliu A, Ferrer E, Riera M, Cifuentes C, Ambrosioni J, Navarro G, Manzardo C, Clotet B, Gatell JM, Casabona J, Miró JM, Murillas J, Manzardo C, Masabeu A, Mercadal J, Cifuentes C, Dalmau D, Domingo P, Falcó V, Curran A, Agustí C, Montoliu A, Pérez I, Curto J, Gargoulas F, Gómez A, Rubia JC, Zamora L, Blanco JL, Garcia-Alcaide F, Martínez E, Mallolas J, Llibre JM, Sirera G, Romeu J, Jou A, Negredo E, Saumoy M, Imaz A, Bolao F, Cabellos C, Peña C, DiYacovo S, Van Den Eynde E, Sala M, Cervantes M, Amengual MJ, Navarro M, Segura V, Barrufet P, Molina J, Alvaro M, Payeras T, Gracia Mateo M, Fernández J. Safe Reduction in CD4 Cell Count Monitoring in Stable, Virally Suppressed Patients With HIV Infection or HIV/Hepatitis C Virus Coinfection. Clin Infect Dis 2016; 62:1578-1585. [PMID: 27126346 DOI: 10.1093/cid/ciw157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/09/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND It has been suggested that routine CD4 cell count monitoring in human immunodeficiency virus (HIV)-monoinfected patients with suppressed viral loads and CD4 cell counts >300 cell/μL could be reduced to annual. HIV/hepatitis C virus (HCV) coinfection is frequent, but evidence supporting similar reductions in CD4 cell count monitoring is lacking for this population. We determined whether CD4 cell count monitoring could be reduced in monoinfected and coinfected patients by estimating the probability of maintaining CD4 cell counts ≥200 cells/µL during continuous HIV suppression. METHODS The PISCIS Cohort study included data from 14 539 patients aged ≥16 years from 10 hospitals in Catalonia and 2 in the Balearic Islands (Spain) since January 1998. All patients who had at least one period of 6 months of continuous HIV suppression were included in this analysis. Cumulative probabilities with 95% confidence intervals were calculated using the Kaplan-Meier estimator stratified by the initial CD4 cell count at the period of continuous suppression initiation. RESULTS A total of 8695 patients were included. CD4 cell counts fell to <200 cells/µL in 7.4% patients, and the proportion was lower in patients with an initial count >350 cells/µL (1.8%) and higher in those with an initial count of 200-249 cells/µL (23.1%). CD4 cell counts fell to <200 cells/µL in 5.7% of monoinfected and 11.1% of coinfected patients. Of monoinfected patients with an initial CD4 cell count of 300-349 cells/µL, 95.6% maintained counts ≥200 cells/µL. In the coinfected group with the same initial count, this rate was lower, but 97.6% of coinfected patients with initial counts >350 cells/µL maintained counts ≥200 cells/µL. CONCLUSIONS From our data, it can be inferred that CD4 cell count monitoring can be safely performed annually in HIV-monoinfected patients with CD4 cell counts >300 cells/µL and HIV/HCV-coinfected patients with counts >350 cells/µL.
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Affiliation(s)
- David Nicolás
- Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona
| | - Anna Esteve
- Centre for Epidemiological Studies on HIV/STI in Catalonia - ASPC, CIBER Epidemiologia y Salud Publica
| | | | - Colin N J Campbell
- Centre for Epidemiological Studies on HIV/STI in Catalonia - ASPC, CIBER Epidemiologia y Salud Publica
| | - Cristina Tural
- Fundació Lluita Contra la Sida, Fundacio Irsicaixa, Hospital Universitari Germans Trias i Pujol
| | - Daniel Podzamczer
- Hospital Universitari de Bellvitge-Bellvitge Institute for Biomedical Research, Hospitalet de Llobregat
| | | | | | - Ferrán Segura
- Corporació Sanitària i Universitària Parc Taulí, Universitat Autónoma de Barcelona
| | | | | | | | | | | | - Alexandra Montoliu
- Centre for Epidemiological Studies on HIV/STI in Catalonia - ASPC, CIBER Epidemiologia y Salud Publica
| | - Elena Ferrer
- Hospital Universitari de Bellvitge-Bellvitge Institute for Biomedical Research, Hospitalet de Llobregat
| | | | | | - Juan Ambrosioni
- Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona
| | - Gemma Navarro
- Corporació Sanitària i Universitària Parc Taulí, Universitat Autónoma de Barcelona
| | - Christian Manzardo
- Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona
| | - Bonaventura Clotet
- Hospital Universitari de Bellvitge-Bellvitge Institute for Biomedical Research, Hospitalet de Llobregat
| | - Josep M Gatell
- Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona
| | - Jordi Casabona
- Centre for Epidemiological Studies on HIV/STI in Catalonia - ASPC, CIBER Epidemiologia y Salud Publica
| | - José M Miró
- Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona
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30
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Faivre-Rampant P, Zaina G, Jorge V, Giacomello S, Segura V, Scalabrin S, Guérin V, De Paoli E, Aluome C, Viger M, Cattonaro F, Payne A, PaulStephenRaj P, Le Paslier MC, Berard A, Allwright MR, Villar M, Taylor G, Bastien C, Morgante M. New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array. Mol Ecol Resour 2016; 16:1023-36. [PMID: 26929265 DOI: 10.1111/1755-0998.12513] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.
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Affiliation(s)
| | - G Zaina
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - V Jorge
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Giacomello
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Segura
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Scalabrin
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Guérin
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - E De Paoli
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - C Aluome
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.,INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Viger
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - F Cattonaro
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - A Payne
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | | | | | - A Berard
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France
| | - M R Allwright
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - M Villar
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - G Taylor
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - C Bastien
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Morgante
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.,IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
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31
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Berlanga P, Segura V, Juan Ribelles A, Sánchez de Toledo P, Acha T, Castel V, Cañete A. Paediatric tumour boards in Spain: a national survey. Clin Transl Oncol 2015; 18:931-6. [PMID: 26693730 DOI: 10.1007/s12094-015-1466-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/07/2015] [Indexed: 10/22/2022]
Abstract
PURPOSE Multidisciplinary tumour boards (MDTs) are conducted worldwide for the management of patients with cancer, and they deliver a higher standard of care by simultaneously involving different specialists in diagnosis and treatment planning. However, information of paediatric MDTs functioning is scarce. A pilot study was conducted in Spain in the frame of the European Expert Paediatric Oncology Reference Network for Diagnostics and Treatment (ExPO-r-Net). METHODS A specific questionnaire was designed regarding various features of MDT practice. Data collected included information on the centres and the team, infrastructure for meetings, MDT organization/logistics and clinical decision-making. The survey was distributed to all Paediatric Oncology Units that register patients in the Spanish Registry of Childhood Tumours (RETI-SEHOP). RESULTS 32 out of 43 contacted centres responded the questionnaire (74 % response rate; 88 % response rate for centres with >25 new patients/year). All units with >25 new patients/year have a dedicated Paediatric MDT compared to 76 % of units with ≤25 new patients/year. MDTs should be improved at institutional level by clear protected time in service planning for all specialists involved, incentives for attendance and attendance registration. Clinical decision-making process and follow-up of recommendation adherence should be assessed and potential legal responsibilities for physicians participating in Tumour Board defined. Network collaboration through virtual MDTs, using available videoconferencing tools, is an opportunity to share expertise among centres.
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Affiliation(s)
- P Berlanga
- Paediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain. .,Instituto de Investigación Sanitaria La Fe, Valencia, Spain.
| | - V Segura
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - A Juan Ribelles
- Paediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain.,Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - P Sánchez de Toledo
- Paediatric Oncology Unit, Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | - T Acha
- Paediatric Oncology Unit, Hospital Carlos Haya, Málaga, Spain
| | - V Castel
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - A Cañete
- Paediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain.,Instituto de Investigación Sanitaria La Fe, Valencia, Spain
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Guillaumet G, Marmol MJ, Sola M, Guzman S, Cuenca L, Segura V. Strategies which ensure our patient’s safety. Intensive Care Med Exp 2015. [PMCID: PMC4798102 DOI: 10.1186/2197-425x-3-s1-a76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Cuadrado-Tejedor M, Garcia-Barroso C, Sanzhez-Arias J, Mederos S, Rabal O, Ugarte A, Franco R, Pascual-Lucas M, Segura V, Perea G, Oyarzabal J, Garcia-Osta A. Concomitant histone deacetylase and phosphodiesterase 5 inhibition synergistically prevents the disruption in synaptic plasticity and it reverses cognitive impairment in a mouse model of Alzheimer's disease. Clin Epigenetics 2015; 7:108. [PMID: 26457123 PMCID: PMC4599811 DOI: 10.1186/s13148-015-0142-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Given the implication of histone acetylation in memory processes, histone deacetylase inhibitors (HDACIs) have been postulated as potential modulators of cognitive impairment in Alzheimer's disease (AD). However, dose-dependent side effects have been described in patients with the currently available broad-spectrum HDACIs, explaining why their therapeutic potential has not been realized for chronic diseases. Here, by simultaneously targeting two independent enzyme activities, histone deacetylase (HDAC) and phosphodiesterase-5 (PDE5), we propose a novel mode of inhibitory action that might increase the therapeutic specificity of HDACIs. RESULTS The combination of vorinostat, a pan-HDACI, and tadalafil, a PDE5 inhibitor, rescued the long-term potentiation impaired in slices from APP/PS1 mice. When administered in vivo, the combination of these drugs alleviated the cognitive deficits in AD mice, as well as the amyloid and tau pathology, and it reversed the reduced dendritic spine density on hippocampal neurons. Significantly, the combination of vorinostat and tadalafil was more effective than each drug alone, both against the symptoms and in terms of disease modification, and importantly, these effects persisted after a 4-week washout period. CONCLUSIONS The results highlight the pharmacological potential of a combination of molecules that inhibit HDAC and PDE5 as a therapeutic approach for AD treatment.
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Affiliation(s)
- M Cuadrado-Tejedor
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 31008 Pamplona, Spain.,Anatomy Department, School of Medicine, University of Navarra, Pamplona, Spain
| | - C Garcia-Barroso
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 31008 Pamplona, Spain
| | - J Sanzhez-Arias
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 55, 31008 Pamplona, Spain
| | - S Mederos
- Cajal Institute, CSIC, Madrid, Spain
| | - O Rabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 55, 31008 Pamplona, Spain
| | - A Ugarte
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 55, 31008 Pamplona, Spain
| | - R Franco
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 31008 Pamplona, Spain.,Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - M Pascual-Lucas
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 31008 Pamplona, Spain
| | - V Segura
- Bioinformatics Unit, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - G Perea
- Cajal Institute, CSIC, Madrid, Spain
| | - J Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 55, 31008 Pamplona, Spain
| | - A Garcia-Osta
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 31008 Pamplona, Spain
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Nuñez M, Nuñez E, Lozano L, Sastre S, Garcia-Cardό A, Segur J, Salό S, Segura V, Sapena N, Alemany X, Montañana J, Cabestany J. FRI0360 User's Experience of a Home- Based Fall-Detecting Device. Ann Rheum Dis 2015. [DOI: 10.1136/annrheumdis-2015-eular.2978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Nuñez E, Sastre S, Lozano L, Garcia-Cardό A, Salό S, Segur J, Sapena N, Segura V, Montañana J, Alemany X, Moreno J, Nuñez M. AB1145 Health-Related Quality of Life in the Elderly Suffering Falls: The Influence of Beliefs on Health and the Fear of Falling. Ann Rheum Dis 2015. [DOI: 10.1136/annrheumdis-2015-eular.2998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Nuñez M, Sastre S, Nuñez E, Montañana J, Segura V, Lozano L, Segur J, Alemany X, Moreno J. AB1146 The Relationship Between Function and the Periarticular Knee Structure Measured by Ultrasound in Obese Patients with Knee Osteoarthritis on a Waiting List for Total Knee Replacement. Ann Rheum Dis 2015. [DOI: 10.1136/annrheumdis-2015-eular.2945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Fodor A, Segura V, Denis M, Neuenschwander S, Fournier-Level A, Chatelet P, Homa FAA, Lacombe T, This P, Le Cunff L. Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine. PLoS One 2014; 9:e110436. [PMID: 25365338 PMCID: PMC4217727 DOI: 10.1371/journal.pone.0110436] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/19/2014] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- Agota Fodor
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, Montpellier, France; UMR AGAP, INRA, Montpellier, France
| | | | | | - Samuel Neuenschwander
- University of Lausanne, Department of Ecology and Evolution, Lausanne, Switzerland; University of Lausanne, Swiss Institute of Bioinformatics, Vital-IT, Lausanne, Switzerland
| | | | | | | | | | - Patrice This
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, Montpellier, France; UMR AGAP, INRA, Montpellier, France
| | - Loic Le Cunff
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, Montpellier, France; UMR AGAP, INRA, Montpellier, France
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Flacco N, Segura V, Perez-Aso M, Estrada S, Seller JF, Jiménez-Altayó F, Noguera MA, D'Ocon P, Vila E, Ivorra MD. Different β-adrenoceptor subtypes coupling to cAMP or NO/cGMP pathways: implications in the relaxant response of rat conductance and resistance vessels. Br J Pharmacol 2014; 169:413-25. [PMID: 23373597 DOI: 10.1111/bph.12121] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 01/07/2013] [Accepted: 01/18/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND PURPOSE To analyse the relative contribution of β1 -, β2 - and β3 -adrenoceptors (Adrb) to vasodilatation in conductance and resistance vessels, assessing the role of cAMP and/or NO/cGMP signalling pathways. EXPERIMENTAL APPROACH Rat mesenteric resistance artery (MRA) and aorta were used to analyse the Adrb expression by real-time-PCR and immunohistochemistry, and for the pharmacological characterization of Adrb-mediated activity by wire myography and tissue nucleotide accumulation. KEY RESULTS The mRNAs and protein for all Adrb were identified in endothelium and/or smooth muscle cells (SMCs) in both vessels. In MRA, Adrb1 signalled through cAMP, Adrb3 through both cAMP and cGMP, but Adrb2, did not activate nucleotide formation; isoprenaline relaxation was inhibited by propranolol (β1 , β2 ), CGP20712A (β1 ), and SQ22536 (adenylyl cyclase inhibitor), but not by ICI118,551 (β2 ), SR59230A (β3 ), ODQ (soluble guanylyl cyclase inhibitor), L-NAME or endothelium removal. In aorta, Adrb1 signalled through cAMP, while β2 - and β3 -subtypes through cGMP; isoprenaline relaxation was inhibited by propranolol, ICI118,551, ODQ, L-NAME, and to a lesser extent, by endothelium removal. CL316243 (β3 -agonist) relaxed aorta, but not MRA. CONCLUSION AND IMPLICATION Despite all three Adrb subtypes being found in both vessels, Adrb1, located in SMCs and acting through the adenylyl cyclase/cAMP pathway, are primarily responsible for vasodilatation in MRA. However, Adrb-mediated vasodilatation in aorta is driven by endothelial Adrb2 and Adrb3, but also by the Adrb2 present in SMCs, and is coupled to the NO/cGMP pathway. These results could help to understand the different physiological roles played by Adrb signalling in regulating conductance and resistance vessels.
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Affiliation(s)
- N Flacco
- Departament de Farmacologia, Facultat de Farmacia, Universitat de Valencia, Burjassot, Spain
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Sauvage C, Segura V, Bauchet G, Stevens R, Do PT, Nikoloski Z, Fernie AR, Causse M. Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits. Plant Physiol 2014; 165:1120-1132. [PMID: 24894148 PMCID: PMC4081326 DOI: 10.1104/pp.114.241521] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.
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Affiliation(s)
- Christopher Sauvage
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
| | - Vincent Segura
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
| | - Guillaume Bauchet
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
| | - Rebecca Stevens
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
| | - Phuc Thi Do
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
| | - Zoran Nikoloski
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
| | - Alisdair R Fernie
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
| | - Mathilde Causse
- Institut National de la Recherche Agronomique, UR1052, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet cedex, France (C.S., G.B., R.S., M.C.);Institut National de la Recherche Agronomique, UR0588, 45075 Orleans cedex 2, France (V.S.);Syngenta Seeds, 31790 Saint Sauveur, France (G.B.);Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (P.T.D., Z.N., A.R.F.); andFaculty of Biology, University of Science, Vietnam National University, Thanh Xuan, Hanoi, Vietnam (P.T.D.)
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Nuñez M, Sastre S, Nuñez E, Saulό A, Segur J, Maurits N, Moreno M, Cabestany J, Segarra J, Segura V, Lozano L, Alemany X, Maculé F, Suso S. SAT0435 Knee Osteoarthritis and Periarticular Structure Quantified by Ultrasound. A Case-Control Study. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2014-eular.3136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Perez-Aso M, Segura V, Montó F, Barettino D, Noguera MA, Milligan G, D'Ocon P. The three α1-adrenoceptor subtypes show different spatio-temporal mechanisms of internalization and ERK1/2 phosphorylation. Biochim Biophys Acta 2013; 1833:2322-33. [PMID: 23797059 DOI: 10.1016/j.bbamcr.2013.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 12/21/2022]
Abstract
We analyzed the kinetic and spatial patterns characterizing activation of the MAP kinases ERK 1 and 2 (ERK1/2) by the three α1-adrenoceptor (α1-AR) subtypes in HEK293 cells and the contribution of two different pathways to ERK1/2 phosphorylation: protein kinase C (PKC)-dependent ERK1/2 activation and internalization-dependent ERK1/2 activation. The different pathways of phenylephrine induced ERK phosphorylation were determined by western blot, using the PKC inhibitor Ro 31-8425, the receptor internalization inhibitor concanavalin A and the siRNA targeting β-arrestin 2. Receptor internalization properties were studied using CypHer5 technology and VSV-G epitope-tagged receptors. Activation of α1A- and α1B-ARs by phenylephrine elicited rapid ERK1/2 phosphorylation that was directed to the nucleus and inhibited by Ro 31-8425. Concomitant with phenylephrine induced receptor internalization α1A-AR, but not α1B-AR, produced a maintained and PKC-independent ERK phosphorylation, which was restricted to the cytosol and inhibited by β-arrestin 2 knockdown or concanavalin A treatment. α1D-AR displayed constitutive ERK phosphorylation, which was reduced by incubation with prazosin or the selective α1D antagonist BMY7378. Following activation by phenylephrine, α1D-AR elicited rapid, transient ERK1/2 phosphorylation that was restricted to the cytosol and not inhibited by Ro 31-8425. Internalization of the α1D-AR subtype was not observed via CypHer5 technology. The three α1-AR subtypes present different spatio-temporal patterns of receptor internalization, and only α1A-AR stimulation translates to a late, sustained ERK1/2 phosphorylation that is restricted to the cytosol and dependent on β-arrestin 2 mediated internalization.
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Affiliation(s)
- M Perez-Aso
- Departament de Farmacologia, Universitat de València, Spain
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Townsend T, Segura V, Chigeza G, Penfield T, Rae A, Harvey D, Bowles D, Graham IA. The use of combining ability analysis to identify elite parents for Artemisia annua F1 hybrid production. PLoS One 2013; 8:e61989. [PMID: 23626762 PMCID: PMC3633910 DOI: 10.1371/journal.pone.0061989] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 03/18/2013] [Indexed: 11/24/2022] Open
Abstract
Artemisia annua is an important medicinal crop used for the production of the anti-malarial compound artemisinin. In order to assist in the production of affordable high quality artemisinin we have carried out an A. annua breeding programme aimed at improving artemisinin concentration and biomass. Here we report on a combining ability analysis of a diallel cross to identify robust parental lines for hybrid breeding. The parental lines were selected based on a range of phenotypic traits to encourage heterosis. The general combining ability (GCA) values for the diallel parental lines correlated to the positive alleles of quantitative trait loci (QTL) in the same parents indicating the presence of beneficial alleles that contribute to parental performance. Hybrids generated from crossing specific parental lines with good GCA were identified as having an increase in both artemisinin concentration and biomass when grown either in glasshouse or experimental field trials and compared to controls. This study demonstrates that combining ability as determined by a diallel cross can be used to identify elite parents for the production of improved A. annua hybrids. Furthermore, the selection of material for breeding using this approach was found to be consistent with our QTL-based molecular breeding approach.
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Affiliation(s)
- Theresa Townsend
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Vincent Segura
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Institut National de la Recherche Agronomique, UR0588, Orléans, France
| | - Godfree Chigeza
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Agricultural Research Council: Grain Crops Institute, Potchefstroom, South Africa
| | - Teresa Penfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Research and Knowledge Transfer, University of Exeter, Exeter, United Kingdom
| | - Anne Rae
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- Genetics Department, Cherry Valley Farms Ltd., Caistor, United Kingdom
| | - David Harvey
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Dianna Bowles
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Ian A. Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
- * E-mail:
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Segura V, Medina-Aunon JA, Guruceaga E, Gharbi SI, González-Tejedo C, Sánchez del Pino MM, Canals F, Fuentes M, Casal JI, Martínez-Bartolomé S, Elortza F, Mato JM, Arizmendi JM, Abian J, Oliveira E, Gil C, Vivanco F, Blanco F, Albar JP, Corrales FJ. Spanish human proteome project: dissection of chromosome 16. J Proteome Res 2012; 12:112-22. [PMID: 23234512 DOI: 10.1021/pr300898u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Chromosome 16 Consortium forms part of the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a chromosome-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). A Spanish consortium of 16 laboratories was organized into five working groups: Protein/Antibody microarrays, protein expression and Peptide Standard, S/MRM, Protein Sequencing, Bioinformatics and Clinical healthcare, and Biobanking. The project is conceived on a multicenter configuration, assuming the standards and integration procedures already available in ProteoRed-ISCIII, which is encompassed within HUPO initiatives. The products of the 870 protein coding genes in chromosome 16 were analyzed in Jurkat T lymphocyte cells, MCF-7 epithelial cells, and the CCD18 fibroblast cell line as it is theoretically expected that most chromosome 16 protein coding genes are expressed in at least one of these. The transcriptome and proteome of these cell lines was studied using gene expression microarray and shotgun proteomics approaches, indicating an ample coverage of chromosome 16. With regard to the B/D section, the main research areas have been adopted and a biobanking initiative has been designed to optimize methods for sample collection, management, and storage under normalized conditions and to define QC standards. The general strategy of the Chr-16 HPP and the current state of the different initiatives are discussed.
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Affiliation(s)
- V Segura
- ProteoRed-ISCIII, Center for Applied Medical Research, CIMA, University of Navarra, Pamplona, Spain
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Seren Ü, Vilhjálmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M. GWAPP: a web application for genome-wide association mapping in Arabidopsis. The Plant Cell 2012; 24:4793-805. [PMID: 23277364 PMCID: PMC3556958 DOI: 10.1105/tpc.112.108068] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, small size, short generation time, small genome size, and wide geographic distribution make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire A. thaliana community. To facilitate this, we present GWAPP, an interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.
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Affiliation(s)
- Ümit Seren
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Viena, Austria
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Korte A, Vilhjálmsson BJ, Segura V, Platt A, Long Q, Nordborg M. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet 2012; 44:1066-71. [PMID: 22902788 PMCID: PMC3432668 DOI: 10.1038/ng.2376] [Citation(s) in RCA: 273] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 07/05/2012] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies (GWAS) are a standard approach for studying the genetics of natural variation. A major concern in GWAS is the need to account for the complicated dependence-structure of the data both between loci as well as between individuals. Mixed models have emerged as a general and flexible approach for correcting for population structure in GWAS. Here we extend this linear mixed model approach to carry out GWAS of correlated phenotypes, deriving a fully parameterized multi-trait mixed model (MTMM) that considers both the within-trait and between-trait variance components simultaneously for multiple traits. We apply this to human cohort data for correlated blood lipid traits from the Northern Finland Birth Cohort 1966, and demonstrate greatly increased power to detect pleiotropic loci that affect more than one blood lipid trait. We also apply this to an Arabidopsis dataset for flowering measurements in two different locations, identifying loci whose effect depends on the environment.
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Affiliation(s)
- Arthur Korte
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
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Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet 2012; 44:825-830. [PMID: 22706313 DOI: 10.1038/ng2314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 05/04/2012] [Indexed: 05/25/2023]
Abstract
Population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. Mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but they do not always account for loci of larger effect. Here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. Simulations suggest that our method outperforms existing methods in terms of power as well as false discovery rate. We apply our method to human and Arabidopsis thaliana data, identifying new associations and evidence for allelic heterogeneity. We also show how a priori knowledge from an A. thaliana linkage mapping study can be integrated into our method using a Bayesian approach. Our implementation is computationally efficient, making the analysis of large data sets (n > 10,000) practicable.
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Affiliation(s)
- Vincent Segura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna, Austria
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Vilas-Zornoza A, Agirre X, Abizanda G, Moreno C, Segura V, De Martino Rodriguez A, José-Eneriz ES, Miranda E, Martín-Subero JI, Garate L, Blanco-Prieto MJ, García de Jalón JA, Rio P, Rifón J, Cigudosa JC, Martinez-Climent JA, Román-Gómez J, Calasanz MJ, Ribera JM, Prósper F. Preclinical activity of LBH589 alone or in combination with chemotherapy in a xenogeneic mouse model of human acute lymphoblastic leukemia. Leukemia 2012; 26:1517-26. [PMID: 22307227 DOI: 10.1038/leu.2012.31] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Histone deacetylases (HDACs) have been identified as therapeutic targets due to their regulatory function in chromatin structure and organization. Here, we analyzed the therapeutic effect of LBH589, a class I-II HDAC inhibitor, in acute lymphoblastic leukemia (ALL). In vitro, LBH589 induced dose-dependent antiproliferative and apoptotic effects, which were associated with increased H3 and H4 histone acetylation. Intravenous administration of LBH589 in immunodeficient BALB/c-RAG2(-/-)γc(-/-) mice in which human-derived T and B-ALL cell lines were injected induced a significant reduction in tumor growth. Using primary ALL cells, a xenograft model of human leukemia in BALB/c-RAG2(-/-)γc(-/-) mice was established, allowing continuous passages of transplanted cells to several mouse generations. Treatment of mice engrafted with T or B-ALL cells with LBH589 induced an in vivo increase in the acetylation of H3 and H4, which was accompanied with prolonged survival of LBH589-treated mice in comparison with those receiving vincristine and dexamethasone. Notably, the therapeutic efficacy of LBH589 was significantly enhanced in combination with vincristine and dexamethasone. Our results show the therapeutic activity of LBH589 in combination with standard chemotherapy in pre-clinical models of ALL and suggest that this combination may be of clinical value in the treatment of patients with ALL.
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48
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Nogueira L, Ruiz-Ontañon P, Vazquez-Barquero A, Lafarga M, Berciano MT, Aldaz B, Grande L, Casafont I, Segura V, Robles EF, Suarez D, Garcia LF, Martinez-Climent JA, Fernandez-Luna JL. Blockade of the NFκB pathway drives differentiating glioblastoma-initiating cells into senescence both in vitro and in vivo. Oncogene 2011; 30:3537-48. [PMID: 21423202 DOI: 10.1038/onc.2011.74] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glioblastoma multiforme is one of the most devastating cancers and presents unique challenges to therapy because of its aggressive behavior. Cancer-initiating or progenitor cells have been described to be the only cell population with tumorigenic capacity in glioblastoma. Therefore, effective therapeutic strategies targeting these cells or the early precursors may be beneficial. We have established different cultures of glioblastoma-initiating cells (GICs) derived from surgical specimens and found that, after induction of differentiation, the NFκB transcriptional pathway was activated, as determined by analyzing key proteins such as p65 and IκB and the upregulation of a number of target genes. We also showed that blockade of nuclear factor (NF)κB signaling in differentiating GICs by different genetic strategies or treatment with small-molecule inhibitors, promoted replication arrest and senescence. This effect was partly mediated by reduced levels of the NFκB target gene cyclin D1, because its downregulation by RNA interference reproduced a similar phenotype. Furthermore, these results were confirmed in a xenograft model. Intravenous treatment of immunodeficient mice bearing human GIC-derived tumors with a novel small-molecule inhibitor of the NFκB pathway induced senescence of tumor cells but no ultrastructural alterations of the brain parenchyma were detected. These findings reveal that activation of NFκB may keep differentiating GICs from acquiring a mature postmitotic phenotype, thus allowing cell proliferation, and support the rationale for therapeutic strategies aimed to promote premature senescence of differentiating GICs by blocking key factors within the NFκB pathway.
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Affiliation(s)
- L Nogueira
- Molecular Genetics Unit, Hospital Valdecilla, and Instituto de Formacion e Investigacion Marques de Valdecilla (IFIMAV), Av Cardenal Herrera Oria s/n, Santander, Spain
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Tordera RM, Garcia-García AL, Elizalde N, Segura V, Aso E, Venzala E, Ramírez MJ, Del Rio J. Chronic stress and impaired glutamate function elicit a depressive-like phenotype and common changes in gene expression in the mouse frontal cortex. Eur Neuropsychopharmacol 2011; 21:23-32. [PMID: 20937555 DOI: 10.1016/j.euroneuro.2010.06.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/23/2010] [Accepted: 06/25/2010] [Indexed: 12/24/2022]
Abstract
Major depression might originate from both environmental and genetic risk factors. The environmental chronic mild stress (CMS) model mimics some environmental factors contributing to human depression and induces anhedonia and helplessness. Mice heterozygous for the synaptic vesicle protein (SVP) vesicular glutamate transporter 1 (VGLUT1) have been proposed as a genetic model of deficient glutamate function linked to depressive-like behaviour. Here, we aimed to identify, in these two experimental models, gene expression changes in the frontal cortex, common to stress and impaired glutamate function. Both VGLUT1(+/-) and CMS mice showed helpless and anhedonic-like behavior. Microarray studies in VGLUT1(+/-) mice revealed regulation of genes involved in apoptosis, neurogenesis, synaptic transmission, protein metabolic process or learning and memory. In addition, RT-PCR studies confirmed gene expression changes in several glutamate, GABA, dopamine and serotonin neurotransmitter receptors. On the other hand, CMS affected the regulation of 147 transcripts, some of them involved in response to stress and oxidoreductase activity. Interestingly, 52 genes were similarly regulated in both models. Specifically, a dowregulation in genes that promote cell proliferation (Anapc7), cell growth (CsnK1g1), cell survival (Hdac3), and inhibition of apoptosis (Dido1) was observed. Genes linked to cytoskeleton (Hspg2, Invs), psychiatric disorders (Grin1, MapK12) or an antioxidant enzyme (Gpx2) were also downregulated. Moreover, genes that inhibit the MAPK pathways (Dusp14), stimulate oxidative metabolism (Eif4a2) and enhance glutamate transmission (Rab8b) were upregulated. We suggest that these genes could form part of the altered "molecular context" underlying depressive-like behaviour in animal models. The clinical relevance of these findings is discussed.
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Affiliation(s)
- R M Tordera
- Department of Pharmacology, University of Navarra, 31080 Pamplona, Spain.
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Segura V. Génétique et amélioration d’Artemisia annuaL. pour une production durable d’antipaludiques à base d’artémisinine. Med Sci (Paris) 2010; 26:701-3. [DOI: 10.1051/medsci/2010268-9701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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