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Tricon D, Faivre d'Arcier J, Eyquard JP, Liu S, Decroocq S, Chague A, Liu W, Balakishiyeva G, Mammadov A, Turdiev T, Kostritsyna T, Asma BM, Akparov Z, Decroocq V. Allele mining of eukaryotic translation initiation factor genes in Prunus for the identification of new sources of resistance to sharka. Sci Rep 2023; 13:15247. [PMID: 37709842 PMCID: PMC10502034 DOI: 10.1038/s41598-023-42215-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: 06/09/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Members of the eukaryotic translation initiation complex are co-opted in viral infection, leading to susceptibility in many crop species, including stone fruit trees (Prunus spp.). Therefore, modification of one of those eukaryotic translation initiation factors or changes in their gene expression may result in resistance. We searched the crop and wild Prunus germplasm from the Armeniaca and Amygdalus taxonomic sections for allelic variants in the eIF4E and eIFiso4E genes, to identify alleles potentially linked to resistance to Plum pox virus (PPV). Over one thousand stone fruit accessions (1397) were screened for variation in eIF4E and eIFiso4E transcript sequences which are in single copy within the diploid Prunus genome. We identified new alleles for both genes differing from haplotypes associated with PPV susceptible accessions. Overall, analyses showed that eIFiso4E is genetically more constrained since it displayed less polymorphism than eIF4E. We also demonstrated more variations at both loci in the related wild species than in crop species. As the eIFiso4E translation initiation factor was identified as indispensable for PPV infection, a selection of ten different eIFiso4E haplotypes along 13 accessions were tested by infection with PPV and eight of them displayed a range of reduced susceptibility to resistance, indicating new potential sources of resistance to sharka.
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Affiliation(s)
- David Tricon
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
- INRAE Unité de Recherches 1052 GAFL, 67 allee des Chênes, 84143, Montfavet, France
| | - Julie Faivre d'Arcier
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
- INRAE Unité Expérimentale Domaine des Jarres, 33210, Toulenne, France
| | - Jean-Philippe Eyquard
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Shuo Liu
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou, 115009, Liaoning, China
| | - Stéphane Decroocq
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Aurélie Chague
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Weisheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou, 115009, Liaoning, China
| | - Gulnara Balakishiyeva
- Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education, 11 Izzat Nabiev Str., 1073, Baku, Azerbaijan
| | - Alamdar Mammadov
- Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education, 11 Izzat Nabiev Str., 1073, Baku, Azerbaijan
| | - Timur Turdiev
- Institute of Plant Biology and Biotechnology, Timiryazev Str. 45, 050040, Almaty, Kazakhstan
| | - Tatiana Kostritsyna
- International Higher School of Medicine, 1F Intergelpo Street, 720054, Bishkek, Kyrgyzstan
| | - Bayram M Asma
- Department of Horticulture, Malatya Turgut Ozal University, Malatya, 44210, Turkey
| | - Zeynal Akparov
- Genetic Resources Institute of ANAS, Azadlig Ave. 155, 1106, Baku, Azerbaijan
| | - Véronique Decroocq
- INRAE, UMR 1332 BFP, Virologie, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.
- UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.
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Groppi A, Liu S, Cornille A, Decroocq S, Bui QT, Tricon D, Cruaud C, Arribat S, Belser C, Marande W, Salse J, Huneau C, Rodde N, Rhalloussi W, Cauet S, Istace B, Denis E, Carrère S, Audergon JM, Roch G, Lambert P, Zhebentyayeva T, Liu WS, Bouchez O, Lopez-Roques C, Serre RF, Debuchy R, Tran J, Wincker P, Chen X, Pétriacq P, Barre A, Nikolski M, Aury JM, Abbott AG, Giraud T, Decroocq V. Population genomics of apricots unravels domestication history and adaptive events. Nat Commun 2021; 12:3956. [PMID: 34172741 PMCID: PMC8233370 DOI: 10.1038/s41467-021-24283-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/08/2021] [Indexed: 01/27/2023] Open
Abstract
Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.
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Affiliation(s)
- Alexis Groppi
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, 33077, France
| | - Shuo Liu
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue, Bayuquan District, Yingkou City, 115009, Liaoning, China
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Stéphane Decroocq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Quynh Trang Bui
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - David Tricon
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Sandrine Arribat
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Caroline Belser
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - William Marande
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Jérôme Salse
- INRAE/UBP UMR 1095 GDEC Genetique, Diversite et Ecophysiologie des Cereales, Laboratory PaleoEVO Paleogenomics & Evolution, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Cécile Huneau
- INRAE/UBP UMR 1095 GDEC Genetique, Diversite et Ecophysiologie des Cereales, Laboratory PaleoEVO Paleogenomics & Evolution, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Nathalie Rodde
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Wassim Rhalloussi
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Stéphane Cauet
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Benjamin Istace
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Erwan Denis
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jean-Marc Audergon
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Guillaume Roch
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
- CEP INNOVATION, 23 Rue Jean Baldassini, Lyon, 69364, Cedex 07, France
| | - Patrick Lambert
- INRAE UR1052 GAFL, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, 16802, PA, USA
| | - Wei-Sheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue, Bayuquan District, Yingkou City, 115009, Liaoning, China
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | | | - Rémy-Félix Serre
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Joseph Tran
- EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, Villenave d'Ornon, 33882, France
| | - Patrick Wincker
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Xilong Chen
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Pierre Pétriacq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France
| | - Aurélien Barre
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
| | - Macha Nikolski
- Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, 33076, France
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, 33077, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
| | - Albert Glenn Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY, USA
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay AgroParisTech, Orsay, 91400, France.
| | - Véronique Decroocq
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 71 Av. E. Bourlaux, Villenave d'Ornon, 33140, France.
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3
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Guillaumie S, Decroocq S, Ollat N, Delrot S, Gomès E, Cookson SJ. Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators. BMC Plant Biol 2020; 20:43. [PMID: 31996141 PMCID: PMC6988314 DOI: 10.1186/s12870-020-2258-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/06/2019] [Accepted: 01/20/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Grapevine is a crop of major economic importance, yet little is known about the regulation of shoot development in grapevine or other perennial fruits crops. Here we combine genetic and genomic tools to identify candidate genes regulating shoot development in Vitis spp. RESULTS An F2 population from an interspecific cross between V. vinifera and V. riparia was phenotyped for shoot development traits, and three Quantitative Trait Loci (QTLs) were identified on linkage groups (LGs) 7, 14 and 18. Around 17% of the individuals exhibited a dwarfed phenotype. A transcriptomic study identified four candidate genes that were not expressed in dwarfed individuals and located within the confidence interval of the QTL on LG7. A deletion of 84,482 bp was identified in the genome of dwarfed plants, which included these four not expressed genes. One of these genes was VviCURLY LEAF (VviCLF), an orthologue of CLF, a regulator of shoot development in Arabidopsis thaliana. CONCLUSIONS The phenotype of the dwarfed grapevine plants was similar to that of clf mutants of A. thaliana and orthologues of the known targets of CLF in A. thaliana were differentially expressed in the dwarfed plants. This suggests that CLF, a major developmental regulator in A. thaliana, also controls shoot development in grapevine.
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Affiliation(s)
- Sabine Guillaumie
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France.
| | - Stéphane Decroocq
- UMR1332 BFP, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Nathalie Ollat
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Serge Delrot
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Eric Gomès
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Sarah J Cookson
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
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4
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Liu S, Cornille A, Decroocq S, Tricon D, Chague A, Eyquard JP, Liu WS, Giraud T, Decroocq V. The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events. Mol Ecol 2019; 28:5299-5314. [PMID: 31677192 DOI: 10.1111/mec.15296] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 02/19/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022]
Abstract
Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long-lived perennial fruit trees.
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Affiliation(s)
- Shuo Liu
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France.,Liaoning Institute of Pomology, Yingkou City, China
| | - Amandine Cornille
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - David Tricon
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France
| | - Aurélie Chague
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France
| | | | | | - Tatiana Giraud
- Ecologie Systematique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
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5
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Decroocq S, Cornille A, Tricon D, Babayeva S, Chague A, Eyquard JP, Karychev R, Dolgikh S, Kostritsyna T, Liu S, Liu W, Geng W, Liao K, Asma BM, Akparov Z, Giraud T, Decroocq V. New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance. Mol Ecol 2016; 25:4712-29. [PMID: 27480465 DOI: 10.1111/mec.13772] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 02/28/2016] [Revised: 07/14/2016] [Accepted: 07/25/2016] [Indexed: 12/01/2022]
Abstract
Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.
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Affiliation(s)
- Stéphane Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Amandine Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Tricon
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Sevda Babayeva
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Aurélie Chague
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Jean-Philippe Eyquard
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Raul Karychev
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Svetlana Dolgikh
- Kazakh Research Institute of Horticulture and Viticulture, 238-a Gagarin Avenue, 480060, Almaty, Kazakhstan
| | - Tatiana Kostritsyna
- Botanical Garden of National Academy of Sciences, Akhunbaeva street 1a, 720064, Bishkek, Kyrgyzstan
| | - Shuo Liu
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France.,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.,Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Weisheng Liu
- Liaoning Institute of Pomology, Tiedong Street, Xiongyue Town, Bayuquan District, Yingkou City, Liaoning, 115009, China
| | - Wenjuan Geng
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Kang Liao
- College of Horticulture & Forestry Sciences, Xinjiang Agricultural University, 311 NongDaDong Road, 830052, Urumqi City, Xinjiang, China
| | - Bayram M Asma
- Department of Horticulture, Inonu University, Malatya, 44210, Turkey
| | - Zeynal Akparov
- Genetic Resources Institute of ANAS, Azadlig ave. 155, AZ1106, Baku, Azerbaijan
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.
| | - Véronique Decroocq
- UMR 1332 BFP, Equipe de virologie, INRA, 71 Avenue Edouard Bourlaux, 33882, Villenave d'Ornon, France. .,UMR 1332 BFP, CS20032, Université de Bordeaux, 33882, Villenave d'Ornon, France.
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6
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Mariette S, Wong Jun Tai F, Roch G, Barre A, Chague A, Decroocq S, Groppi A, Laizet Y, Lambert P, Tricon D, Nikolski M, Audergon JM, Abbott AG, Decroocq V. Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca). New Phytol 2016; 209:773-84. [PMID: 26356603 DOI: 10.1111/nph.13627] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 02/04/2015] [Accepted: 07/26/2015] [Indexed: 05/06/2023]
Abstract
In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.
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Affiliation(s)
- Stéphanie Mariette
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
- UMR 1202 BIOGECO, INRA, F-33610, Cestas, France
- UMR 1202 BIOGECO, Université de Bordeaux, F-33400, Talence, France
| | - Fabienne Wong Jun Tai
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Guillaume Roch
- UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France
- CEP INNOVATION, INRA, 23 rue Jean Baldassini, F-69364, LYON Cedex 7, France
| | - Aurélien Barre
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Aurélie Chague
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
| | - Stéphane Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
| | - Alexis Groppi
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Yec'han Laizet
- UMR 1202 BIOGECO, INRA, F-33610, Cestas, France
- UMR 1202 BIOGECO, Université de Bordeaux, F-33400, Talence, France
| | - Patrick Lambert
- UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France
| | - David Tricon
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Jean-Marc Audergon
- UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France
| | - Albert G Abbott
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY, 40546-0073, USA
| | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
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De la Cruz AA, Hilbert G, Mengin V, Rivière C, Ollat N, Vitrac C, Bordenave L, Decroocq S, Delaunay JC, Mérillon JM, Monti JP, Gomès E, Richard T. Anthocyanin phytochemical profiles and anti-oxidant activities of Vitis candicans and Vitis doaniana. Phytochem Anal 2013; 24:446-452. [PMID: 23839937 DOI: 10.1002/pca.2447] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 01/21/2013] [Revised: 04/15/2013] [Accepted: 04/17/2013] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Grapes are one of the most important fruit crops in the world. The quality of red grape berries greatly depends on skin colour, mainly due to the anthocyanin profile. Today, the American Vitis species have the greatest potential for breeding work. They have multiple resistance properties in comparison with Vitis vinifera but little is known about their anthocyanin content. OBJECTIVE To determine the anti-oxidant properties and anthocyanin profile of two American species, Vitis candicans and Vitis doaniana, by using LC-MS(n) and LC-NMR. METHODS Grape extracts were prepared by extraction of berry skins with acidified methanol. The complete structure elucidation of the individual anthocyanins was performed with LC-MS(n) , LC-NMR and NMR experiments. Individual anthocyanins in the extracts were quantified by using malvidin glucoside as external standard. The anti-oxidant activities of grape skin extracts were evaluated by using 1,1-diphenyl-2-picrylhydrazyl (DPPH•) radical scavenging and oxygen radical absorbance capacity (ORAC) assays. RESULTS By using LC-MS(n) and LC-NMR experiments, 30 anthocyanins were identified and quantified in the two Vitis species, including two new cis-p-coumaroyl derivatives. Vitis candicans and V. doaniana showed significant differences in their anthocyanin profile. These two Vitis species possess low-to-medium anti-oxidant activities in comparison with V. vinifera. CONCLUSION The profiles of 30 anthocyanins were established unambiguously in two American Vitis species.
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Guillaumie S, Ilg A, Réty S, Brette M, Trossat-Magnin C, Decroocq S, Léon C, Keime C, Ye T, Baltenweck-Guyot R, Claudel P, Bordenave L, Vanbrabant S, Duchêne E, Delrot S, Darriet P, Hugueney P, Gomès E. Genetic analysis of the biosynthesis of 2-methoxy-3-isobutylpyrazine, a major grape-derived aroma compound impacting wine quality. Plant Physiol 2013; 162:604-15. [PMID: 23606597 PMCID: PMC3668056 DOI: 10.1104/pp.113.218313] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/18/2013] [Indexed: 05/19/2023]
Abstract
Methoxypyrazines (MPs) are strongly odorant volatile molecules with vegetable-like fragrances that are widespread in plants. Some grapevine (Vitis vinifera) varieties accumulate significant amounts of MPs, including 2-methoxy-3-isobutylpyrazine (IBMP), which is the major MP in grape berries. MPs are of particular importance in white Sauvignon Blanc wines. The typicality of these wines relies on a fine balance between the pea pod, capsicum character of MPs and the passion fruit/grapefruit character due to volatile thiols. Although MPs play a crucial role in Sauvignon varietal aromas, excessive concentrations of these powerful odorants alter wine quality and reduce consumer acceptance, particularly in red wines. The last step of IBMP biosynthesis has been proposed to involve the methoxylation of the nonvolatile precursor 2-hydroxy-3-isobutylpyrazine to give rise to the highly volatile IBMP. In this work, we have used a quantitative trait loci approach to investigate the genetic bases of IBMP biosynthesis. This has led to the identification of two previously uncharacterized S-adenosyl-methionine-dependent O-methyltransferase genes, termed VvOMT3 and VvOMT4. Functional characterization of these two O-methyltransferases showed that the VvOMT3 protein was highly specific and efficient for 2-hydroxy-3-isobutylpyrazine methylation. Based on its differential expression in high- and low-MP-producing grapevine varieties, we propose that VvOMT3 is a key gene for IBMP biosynthesis in grapevine.
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Affiliation(s)
| | | | - Stéphane Réty
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Maxime Brette
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Claudine Trossat-Magnin
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Stéphane Decroocq
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Céline Léon
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Céline Keime
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Tao Ye
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Raymonde Baltenweck-Guyot
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Patricia Claudel
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Louis Bordenave
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Sandra Vanbrabant
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Eric Duchêne
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
| | - Serge Delrot
- Université de Bordeaux and Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, Unité Mixte de Recherche 1287, F–33140 Villenave d’Ornon, France (S.G., C.T.-M., S.Dec., C.L., L.B., S.Del., E.G.)
- Université de Strasbourg, F–67081 Strasbourg, France (A.I., R.B.-G., P.C., E.D., P.H.)
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8015 Laboratoire de Cristallographie et Résonance Magnétique Nucléaire Biologiques, Université Paris Descartes, F–75270 Paris, France (S.R.)
- Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Equipe d’Accueil 4577 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Institut des Sciences de la Vigne et du Vin, Unité Sous Contrat 1366 Œnologie, F–33140 Villenave d’Ornon, France (M.B., S.V., P.D.)
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1131 Santé de la Vigne et Qualité du Vin, F–68021 Colmar, France (A.I., R.B.-G., P.C., E.D., P.H.); and
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, F–67404 Illkirch, France (C.K., T.Y.)
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Bert PF, Bordenave L, Donnart M, Hévin C, Ollat N, Decroocq S. Mapping genetic loci for tolerance to lime-induced iron deficiency chlorosis in grapevine rootstocks (Vitis sp.). Theor Appl Genet 2013; 126:451-73. [PMID: 23139142 DOI: 10.1007/s00122-012-1993-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/21/2012] [Indexed: 05/24/2023]
Abstract
Iron is essential to plants for chlorophyll formation as well as for the functioning of various iron-containing enzymes. Iron deficiency chlorosis is a wide-spread disorder of plants, in particular, of those growing on calcareous soils. Among the different ways to control iron deficiency problems for crops, plant material and especially rootstock breeding is a suitable and reliable method, especially for fruit trees and grapes. The aim of the experiment was to characterize the genetic basis of grapevine chlorosis tolerance under lime stress conditions. A segregating population of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera Cabernet Sauvignon (tolerant) × V. riparia Gloire de Montpellier (sensitive) was developed and phenotyped both as cuttings and as rootstock grafted with Cabernet Sauvignon scions in pots containing non-chlorosing and chlorosing soils. Tolerance was evaluated by chlorosis score, leaf chlorophyll content and growth parameters of the shoots and roots. The experiments were performed in 2001, 2003 and 2006. The plants analysed in 2006 were reassessed in 2007. The most significant findings of the trial were: (a) the soil properties strongly affect plant development, (b) there are differences in tolerance among segregating genotypes when grown as cuttings or as rootstocks on calcareous soil, (c) calcareous conditions induced chlorosis and revealed quantitative trait loci (QTLs) implicated in polygenic control of tolerance, (d) rootstock strongly contributes to lime-induced chlorosis response, and (e) a QTL with strong effect (from 10 to 25 % of the chlorotic symptom variance) was identified on chromosome 13. This QTL colocalized with a QTL for chlorophyll content (R (2) = 22 %) and a major QTL for plant development that explains about 50 % of both aerial and root system biomass variation. These findings were supported by stable results among the different years of experiment. These results open new insights into the genetic control of chlorosis tolerance and could aid the development of iron chlorosis-tolerant rootstocks.
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Affiliation(s)
- Pierre-François Bert
- INRA, Univ. Bordeaux, ISVV, Ecophysiology and Functional Genomics of Grapevine, UMR 1287, 33140 Villenave d'Ornon, France.
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Marguerit E, Boury C, Manicki A, Donnart M, Butterlin G, Némorin A, Wiedemann-Merdinoglu S, Merdinoglu D, Ollat N, Decroocq S. Genetic dissection of sex determinism, inflorescence morphology and downy mildew resistance in grapevine. Theor Appl Genet 2009; 118:1261-78. [PMID: 19238349 DOI: 10.1007/s00122-009-0979-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 01/22/2009] [Indexed: 05/20/2023]
Abstract
A genetic linkage map of grapevine was constructed using a pseudo-testcross strategy based upon 138 individuals derived from a cross of Vitis vinifera Cabernet Sauvignon x Vitis riparia Gloire de Montpellier. A total of 212 DNA markers including 199 single sequence repeats (SSRs), 11 single strand conformation polymorphisms (SSCPs) and two morphological markers were mapped onto 19 linkage groups (LG) which covered 1,249 cM with an average of 6.7 cM between markers. The position of SSR loci in the maps presented here is consistent with the genome sequence. Quantitative traits loci (QTLs) for several traits of inflorescence and flower morphology, and downy mildew resistance were investigated. Two novel QTLs for downy mildew resistance were mapped on linkage groups 9 and 12, they explain 26.0-34.4 and 28.9-31.5% of total variance, respectively. QTLs for inflorescence morphology with a large effect (14-70% of total variance explained) were detected close to the Sex locus on LG 2. The gene of the enzyme 1-aminocyclopropane-1-carboxylic acid synthase, involved in melon male organ development and located in the confidence interval of all QTLs detected on the LG 2, could be considered as a putative candidate gene for the control of sexual traits in grapevine. Co-localisations were found between four QTLs, detected on linkage groups 1, 14, 17 and 18, and the position of the floral organ development genes GIBBERELLIN INSENSITIVE1, FRUITFULL, LEAFY and AGAMOUS. Our results demonstrate that the sex determinism locus also determines both flower and inflorescence morphological traits.
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Affiliation(s)
- Elisa Marguerit
- Université de Bordeaux, UMR Ecophysiologie et Génomique Fonctionelle de la Vigne, Gradignan, France
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Oddou-Muratorio S, Aligon C, Decroocq S, Plomion C, Lamant T, Mush-Demesure B. Microsatellite primers for Sorbus torminalis
and related species. ACTA ACUST UNITED AC 2005. [DOI: 10.1046/j.1471-8278.2001.00116.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Langrell SRH, Lung-Escarmant B, Decroocq S. Isolation and characterization of polymorphic simple sequence repeat loci in Armillaria ostoyae. ACTA ACUST UNITED AC 2005. [DOI: 10.1046/j.1471-8278.2001.00119.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Androgenesis, the development of a haploid embryo from a male nucleus, has been shown to result in the instantaneous uncoupling of the transmission of the organelle and nuclear genomes (with the nuclear genome originating from the male parent only and the organelle genomes from the female parent). We report, for the first time, uncoupling resulting from gynogenesis, in Actinidia deliciosa (kiwifruit), a plant species known for its paternal mode of chloroplast inheritance. After pollen irradiation, transmission of nuclear genes from the pollen parent to the progeny was inhibited, but transmission of the chloroplast genome was not. This demonstrates that plastids can be discharged from the pollen tube into the egg with little or no concomitant transmission of paternal nuclear genes. Such events of opposite inheritance of the organelle and nuclear genomes must be very rare in nature and are unlikely to endanger the long-term stability of the association between the different genomes of the cell. However, they could lead to incongruences between organelle gene trees and species trees and may constitute an alternative to the hybridization/introgression scenario commonly invoked to account for such incongruences.
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Affiliation(s)
- Joëlle Chat
- Unité de Recherches sur les Espèces Fruitières et la Vigne, INRA, B.P. 81, F-33883 Villenave d'Ornon Cedex, France.
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Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S. Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 2003; 106:912-922. [PMID: 12647067 DOI: 10.1007/s00122-002-1158-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2002] [Accepted: 08/23/2002] [Indexed: 05/24/2023]
Abstract
EST microsatellite markers were developed in apricot (Prunus armeniaca L.) and grape (Vitis vinifera L.). cDNA libraries from either apricot leaves or grape roots were used in an enrichment procedure for GA and CA repeats. The transferability of EST simple sequence repeat (SSR) markers from apricot and grapevine to other related and unrelated species was examined. Overall, grape primers amplified products in most of the Vitaceae accessions while the apricot primers amplified polymorphic alleles only in closely related species of the Rosaceae. In this taxonomic family, ten EST SSR loci were tested, and one single primer pair, PacB22, was amplified across species and sections in the Prunoideae and Maloideae. Sequencing of EST SSR loci in other species and genera confirmed a higher level of conservation in the microsatellite motif and flanking regions in the Vitaceae compared to the Rosaceae. Two distinct fragments of the PacB22 locus amplified across the Malus and Pyrus genera; however, while the coding region was highly conserved, the microsatellite repeat motif was no longer present. The banding pattern was explained by base substitution and insertion/deletion events in the intronic region of PacB22. This study includes the determination of the degree of polymorphism detected among species and genera in two unrelated taxonomic families and the evaluation of the information provided by the microsatellite repeats and the flanking regions.
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Affiliation(s)
- V Decroocq
- INRA Centre de Bordeaux, U.R.E.F.V, 71 Avenue E. Bourleaux, 33883 Villenave d'Ornon France.
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Lowe AJ, Goodall-Copestake WP, Caron H, Kremer A, Decroocq S. A set of polymorphic microsatellites for Vochysia ferruginea, a promising tree for land reclamation in the Neotropics. ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2002.00192.x] [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: 11/20/2022]
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Latouche-Halle C, Ramboer A, Bandou E, Caron H, Decroocq S. Isolation and characterization of microsatellite markers in the tropical tree species Dicorynia guianensis (Caesalpinaceae). ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2002.00196.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chat J, Decroocq S, Decroocq V, Petit RJ. A case of chloroplast heteroplasmy in kiwifruit (Actinidia deliciosa) that is not transmitted during sexual reproduction. J Hered 2002; 93:293-300. [PMID: 12407220 DOI: 10.1093/jhered/93.4.293] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the first case of plastid chimera within the Actinidia genus, where plastid inheritance was believed to be paternal. The heterogeneity of chloroplast DNA observed in the hexaploid Actinidia deliciosa cultivar D uno involves the presence or absence of a particular MspI restriction site in the region between the psbC gene and the tRNA-Ser(UGA) gene. The heterogeneity was first observed using restriction fragment length polymorphism and then confirmed through cloning and sequencing. The analysis of the cloned fragments revealed the presence of two haplotypes: the most frequent type was found in 123 (88.5%) out of a total of 139 colonies screened. Partial sequences of the psbC-trnS fragment from both haplotypes revealed that the polymorphism occurs within the coding region of the psbC gene and consists of a synonymous transition. A contamination-free cross involving D uno as the male parent produced only plants characterized by the most frequent haplotype, indicating either selection bias against the rare type or more likely fixation of the frequent type in tissues leading to the formation of the male gametes. The MspI restriction profiles performed on various tissues suggest that the rarer type is absent from the histogenic layer LII and that D uno is a periclinal plastid chimera.
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Affiliation(s)
- J Chat
- Unité de Recherches sur les Espèces Fruitières et la Vigne, INRA, B P 81, F-33883 Villenave d'Ornon Cedex, France.
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Decroocq-Ferrant V, Decroocq S, Van Went J, Schmidt E, Kreis M. A homologue of the MAP/ERK family of protein kinase genes is expressed in vegetative and in female reproductive organs of Petunia hybrida. Plant Mol Biol 1995; 27:339-350. [PMID: 7888623 DOI: 10.1007/bf00020188] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The mitogen activated protein (MAP) kinase pathway of eukaryotes is stimulated by many growth factors and is required for the integration of multiple cellular signals. In order to study the function of MAP kinases during plant ovule development we have synthesized a Petunia hybrida ovule-specific cDNA library and screened for MAP protein kinase-related sequences using a DNA probe obtained by PCR. A full-length cDNA clone was identified (PMEK for Petunia hybrida MAP/ERK-related protein kinase) and shown to encode a protein related to the family of MAP/ERK protein kinases. Southern blot analysis showed that PMEK is a member of a small multigene family in P. hybrida. The cDNA codes for a protein (PMEK1) of 44.4 kDa with an overall sequence identity of 44% to the products of the mammalian ERK/MAP kinase gene, and the budding yeast KSS1 and FUS3 genes. PMEK1 displays 96 and 80% identity respectively with the tobacco NTF3 and Arabidopsis ATMPK1 kinases, and only 50% to the more distantly related plant MAP kinase MsERK1 from alfalfa. The two phosphorylation sites found in the loop between subdomain VII and VIII in all the other MAP kinases are also present in PMEK1. RNA gel blot and RT-PCR analyses demonstrated that PMEK1 is expressed in vegetative organs and preferentially accumulated in female reproductive organs of P. hybrida. In situ hybridization experiments showed that in the reproductive organs PMEK1 is expressed only in the ovary and not in the stamen.
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Affiliation(s)
- V Decroocq-Ferrant
- Université de Paris-Sud, IBP, URA-CNRS 1128, Biologie du Développement des Plantes, Orsay, France
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