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1. Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

Author

Hélène Muranty, Caroline Denancé, Laurence Feugey, Jean-Luc Crépin, Yves Barbier, Stefano Tartarini, Matthew Ordidge, Michela Troggio, Marc Lateur, Hilde Nybom, Frantisek Paprstein, François Laurens, and Charles-Eric Durel

Subjects
Malus domestica, Genotyping, Parentage analysis, Parent-offspring, Founders, Germplasm collection, Botany, QK1-989
Abstract

Abstract Background Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees. Results Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as ‘Ribston Pippin’, ‘White Transparent’ and ‘Braeburn’ were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely ‘Reinette Franche’ and ‘Margil’, and one North-Eastern Europe cultivar from the 1700s, ‘Alexander’. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards. Conclusions The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.

Published
2020
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2. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

Author

Jorge Urrestarazu, Hélène Muranty, Caroline Denancé, Diane Leforestier, Elisa Ravon, Arnaud Guyader, Rémi Guisnel, Laurence Feugey, Sébastien Aubourg, Jean-Marc Celton, Nicolas Daccord, Luca Dondini, Roberto Gregori, Marc Lateur, Patrick Houben, Matthew Ordidge, Frantisek Paprstein, Jiri Sedlak, Hilde Nybom, Larisa Garkava-Gustavsson, Michela Troggio, Luca Bianco, Riccardo Velasco, Charles Poncet, Anthony Théron, Shigeki Moriya, Marco C. A. M. Bink, François Laurens, Stefano Tartarini, and Charles-Eric Durel

Subjects
adaptive traits, association genetics, germplasm collection, GWAS, Malus × domestica Borkh., microsynteny, Plant culture, SB1-1110
Abstract

Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.

Published
2017
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3. New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties.

Author

Amandine Cornille, Pierre Gladieux, Marinus J M Smulders, Isabel Roldán-Ruiz, François Laurens, Bruno Le Cam, Anush Nersesyan, Joanne Clavel, Marina Olonova, Laurence Feugey, Ivan Gabrielyan, Xiu-Guo Zhang, Maud I Tenaillon, and Tatiana Giraud

Subjects
Genetics, QH426-470
Abstract

The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.

Published
2012
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4. Conservation of horticultural genetic resources in France

Author

Michel Roux-Cuvelier, Michel Grisoni, Arnaud Bellec, Emmanuel Bloquel, Carine Charron, Magalie Delalande, Marine Delmas, Audrey Didier, Charles-Eric Durel, Charles-Henry Duval, Florence Esnault, Laurence Feugey, Emmanuel Geoffriau, Bouchaib Khadari, Sandra Lepers-Andrzejewski, Luro François, Cécile Marchal, Alix Pernet, Jérémy Salinier, Marc Seguin, Rebecca Stevens, Bernice van Issum-Groyer, Rémi Kahane, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Génétique et Amélioration des Fruits et Légumes (GAFL), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Citrus, Unité Expérimentale Arboricole (UE ARBO), Institut National de la Recherche Agronomique (INRA), Université des Antilles - UFR des sciences médicales Hyacinthe Bastaraud (UA UFR SM), Université des Antilles (UA), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Unité expérimentale du GEVES, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Etablissement Vanille de Tahiti, Partenaires INRAE, Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales Corse - Antenne Corse (AGAP-Corse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Domaine expérimental de Vassal (MONTP DOM VASSAL), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Unité d'arboriculture (BORDX ARBORI UE)

Subjects
agrobiodiversité, [SDV]Life Sciences [q-bio], Horticulture, Conservation des ressources génétiques, F30 - Génétique et amélioration des plantes, Ressource génétique végétale, F01 - Culture des plantes, Conservation du matériel génétique, Conservation de la diversité biologique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

5. Genome wide association study of two phenology traits (flowering time and maturity date) in apple

Author

Diane Leforestier, Marco C. A. M. Bink, Laurence Feugey, Matthew Ordidge, Charles Poncet, Luca Bianco, Elisa Ravon, Jorge Urrestarazu, Frantisek Paprstein, Larisa Garkava-Gustavsson, Caroline Denancé, Helene Muranty, Charles-Eric Durel, Stefano Tartarini, Riccardo Velasco, Arnaud Guyader, Anthony Théron, M. Troggio, Luca Dondini, Marc Lateur, Jiri Sedlak, Roberto Gregori, François Laurens, Hilde Nybom, Rémi Guisnel, Patrick Houben, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), S. Tartarini, H. Nybom, F. Laurens, L. Dondini, Muranty, H., Urrestarazu, J., Denancã©, C., Leforestier, D., Ravon, E., Guyader, A., Guisnel, R., Feugey, L., Tartarini, Stefano, Dondini, Luca, Gregori, Roberto, Lateur, M., Houben, P., Sedlak, J., Paprstein, F., Ordidge, M., Nybom, H., Garkava-gustavsson, L., Troggio, M., Bianco, L., Velasco, R., Poncet, C., Thã©ron, A., Bink, M. C. A. M., Laurens, F., Durel, C. E., Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, Linkage disequilibrium, [SDV]Life Sciences [q-bio], Single-nucleotide polymorphism, Genome-wide association study, Biology, Quantitative trait locus, Horticulture, 01 natural sciences, 03 medical and health sciences, Malus × domestica, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Germplasm collection, Malus x domestica, 2. Zero hunger, Genetics, Phenology, fungi, food and beverages, Marker-assisted selection, PE&RC, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Biometris, 030104 developmental biology, Germplasm collections, Trait, germplasm collections, 010606 plant biology & botany
Abstract

International audience; The aim of Genome Wide Association Studies (GWAS) is to identify markers in tight linkage disequilibrium with loci controlling quantitative trait variation. These markers can then be used in marker-assisted selection (MAS) in fruit crops such as apple. The GWAS approach involves both phenotyping of a large population of mostly unrelated individuals for the traits of interest, and genotyping at high marker density. In the EU-FP7 project FruitBreedomics, almost 1,200 European diploid dessert apple accessions (old and/or local cultivars) from six germplasm collections were genotyped with the Affymetrix Axiom_Apple480K array (487,000 SNPs). Phenotypic data on a large number of traits have been gathered during the project. Here we focus on flowering period and harvesting date. Knowledge of the genetic control of these traits is necessary to develop cultivars that can face the challenges imposed by global climate change and to target cultivar development as a function of a prolonged vegetation period in the production regions. Different models were tested, including control for effects of population structure and relatedness between cultivars. The full model, controlling for both structure and relatedness, was shown to be the most appropriate to avoid spurious marker-trait associations. When analyzing data over all collections, one significant marker-trait association was obtained for each trait, on chromosomes 9 and 3, for flowering period and harvesting date, respectively. Thereby, genomic locations previously identified in bi-parental populations could now be confirmed for a genetically diverse germplasm.

Published
2017
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6. Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

Author

Pauline Lasserre-Zuber, Laurence Hibrand-Saint-Oyant, Charles Poncet, Caroline Denancé, Elisa Ravon, Charles-Eric Durel, Laurence Feugey, Ludivine Lassois, Rémi Guisnel, Arnaud Guyader, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), BIOSystem Engineering (BIOSE) Department, Université de Liège, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), FRB (Fondation pour la Recherche sur la Biodiversité) 'CorePom' AAP-IN-2009-14, Région Pays de la Loire, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, [SDV]Life Sciences [q-bio], Population structure, Plant Science, Biology, 01 natural sciences, diversity, Loss of heterozygosity, 03 medical and health sciences, Malus × domestica, Botany, genetic structure, Allelic diversity, Cultivar, Molecular Biology, Selection (genetic algorithm), 2. Zero hunger, Genetic diversity, SSR, 030104 developmental biology, Evolutionary biology, Genetic structure, parentage analysis, core collection, 010606 plant biology & botany
Abstract

In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P (ID) over the 21 retained SSR loci close to 10−28. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H e of 0.82 and observed heterozygosity H o of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014–0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as “King of Pippin” and “Calville Rouge d’Hiver” as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity.

Published
2016
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7. New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties

Author

Joanne Clavel, Maud I. Tenaillon, Marina V. Olonova, Amandine Cornille, Ivan Gabrielyan, Marinus J. M. Smulders, Xiu-Guo Zhang, Anush Nersesyan, Pierre Gladieux, Laurence Feugey, Tatiana Giraud, Isabel Roldán-Ruiz, François Laurens, Bruno Le Cam, Томский государственный университет Институт биологии, экологии, почвоведения, сельского и лесного хозяйства (Биологический институт) Кафедра экологического менеджмента, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Plant Res Int, Wageningen University and Research [Wageningen] (WUR), Growth & Dev Grp, Plant Sci Unit, Research Institute for Agricultural, Fisheries and Food (ILVO), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Dept Plant Taxon, Inst Bot, National Academy of Sciences of the Republic of Armenia [Yerevan] (NAS RA), Region Ile de France (PICRI), IDEEV, Fondation Dufrenoy, SBF (Societe Botanique de France), Groupe de Recherche ComEvol, Wageningen University and Research Centre [Wageningen] (WUR), Institute for Agricultural and Fisheries Research, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), and National Academy of Sciences of Armenia

Subjects
0106 biological sciences, Evolutionary Genetics, Cancer Research, Plant Evolution, [SDV]Life Sciences [q-bio], population-structure, Plant Science, Breeding, геном растений, Plant Genetics, 01 natural sciences, Gene flow, genetische diversiteit, allele frequency data, domesticatie, Genetics (clinical), 2. Zero hunger, malus domestica, 0303 health sciences, biology, Agriculture, Forestry, genetic diversity, spondias-purpurea, Europe, pomme, Phylogeography, wild relatives, Malus, évolution du génome, voorouders, генетическая изменчивость, Genome, Plant, Research Article, Gene Flow, China, Asia, фрукты, lcsh:QH426-470, introgression, ancestors, plant genetic resources, flux de gènes, Introgression, fruit tree, appels, Crops, analyse phylogénétique, Crop, Molecular Genetics, Evolution, Molecular, 03 medical and health sciences, domestication, wilde verwanten, Botany, sylvestris l. mill, Genetics, Domestication, Molecular Biology, Biology, Ecology, Evolution, Behavior and Systematics, apples, 030304 developmental biology, Genetic diversity, genus malus, Evolutionary Biology, multilocus genotype data, fungi, Genetic Variation, 15. Life on land, microsatellite markers, biology.organism_classification, lcsh:Genetics, Plant Breeding, genetische bronnen van plantensoorten, Malus sieversii, Spain, Fruit, генетика, Population Genetics, 010606 plant biology & botany, approximate bayesian computation, molecular-genetics, Microsatellite Repeats
Abstract

The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species., Author Summary The apple, one of the most ubiquitous and culturally important temperate fruit crops, provides us with a unique opportunity to study the process of domestication in trees. The number and identity of the progenitors of the domesticated apple and the erosion of genetic diversity associated with the domestication process remain debated. The Central Asian wild apple has been identified as the main progenitor, but other closely related species along the Silk Route running from Asia to Western Europe may have contributed to the genome of the domesticated crop. Using rapidly evolving genetic markers to make inferences about the recent evolutionary history of the domesticated apple, we found that the European crabapple has made an unexpectedly large contribution to the genome of the domesticated apple. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the domesticated apple being currently more similar genetically to this secondary genepool than to the ancestral progenitor, the Central Asian wild apple. We found that domesticated apples have evolved over long time scales, with contributions from at least two wild species in different geographic areas, with no significant erosion of genetic diversity. This process of domestication and diversification may be common to other fruit trees and contrasts with the models documented for annual crops.

Published
2012
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8. The devastating but well understood Dutch elm disease (Graphium ceratocystis ulmi)

Author

J. Pinon, Laurence Feugey, Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
0106 biological sciences, Forestry, 04 agricultural and veterinary sciences, Biology, 040401 food science, 01 natural sciences, 0404 agricultural biotechnology, ORME, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, LUTTE, [SDE]Environmental Sciences, [SDV.SA.SF] Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany
Abstract

International audience

Published
1994
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9. 146. Cryopreservation of French plant genetic resource collections (CRYOVEG)

Author

Yann Froelicher, Laurence Feugey, André Peyrière, Suzia Rubens, Teresa Barreneche, Jocelyne Sapotille, Emilie Balsemin, Danièle Roques, Michel Grisoni, François Luro, Bernard Moulin, Lydie Fouilhaux, Emmanuel Couturon, Yvon Prigent, Franck Curk, Jean-Eric Chauvin, Alain Label, David Teyssedre, Franciane Gamiette, Florent Engelmann, Arnaud Guyader, Martine Muller, Agnès Grapin, Philippe Guérif, Philippe Chatelet, Michel Roux-Cuvelier, Catherine Souchet, Jean-Paul Dantec, Stéphane Dussert, Marie-Ange Dantec, and Michel Renard

Subjects
PEAR, Resource (biology), Agroforestry, business.industry, Coffea, General Medicine, Biology, biology.organism_classification, General Biochemistry, Genetics and Molecular Biology, Cryopreservation, Biotechnology, Work (electrical), Genetic resources, Agriculture, Action plan, General Agricultural and Biological Sciences, business
Abstract

In France, cryopreservation is currently used for a limited number of forest tree species, but has been applied yet very little to horticultural or other agricultural species. The CRYOVEG project aims at (1) developing or optimizing cryopreservation techniques in a range of selected species; and (2) establishing a national scientific and technical network of plant biological resource centers (CRBs) using cryopreservation. The project has a network organization, with IRD/INRA Montpellier as the cryopreservation expertise centre and partners in continental France and in overseas departments in charge of genetic resource conservation for various species: INRA Petit Bourg, Guadeloupe (yam); INRA San Giuliano, Corsica (Citrus); INRA Bordeaux (Prunus); INRA Angers (apple and pear); INRA Montpellier (grapevine); INRA Ploudaniel (potato, Brassica); IRD La Reunion (coffee); CIRAD Roujol, Guadeloupe (sugarcane); and CIRAD La Reunion (vanilla, garlic). Deliverables will vary depending on the state-of-the-art of cryopreservation for each species: for potato, yam, sugarcane, garlic, Citrus, Brassica and coffee, optimized protocols will be tested on a range of representative accessions. For grapevine, Prunus, apple, pear and vanilla, operational protocols will be developed. The group will work as a think-tank on the integration of cryopreservation in the national plant genetic resource conservation strategy and an action plan for its implementation will be collectively designed. The project will work towards establishing a French research network on plant genetic resource cryopreservation, open to all partners interested in cryopreservation. The group will prepare research and development projects whose results will be disseminated through European plant genetic resource conservation networks e.g. ECP/ GR). Finally, network members will train French and foreign (from North and South countries) researchers and technicians in cryopreservation techniques. (Conflicts of interest: None declared. Source of funding: This project is supported by a French competitive grant (Call for Projects 2008 ''Biological Resource Centers") of the Consultative Committee for Biological Resources/Infrastructures in the Biology, Health and Agronomy sectors (CCRB/IBiSA).). (Texte integral)

Published
2009
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10. Comparative analysis of the duplication degree and genetic relationships between three apple collections located in the Pyrenean region

Author

Luis G. Santesteban, E. Leterme, Laurence Feugey, Caroline Denancé, Jorge Urrestarazu, Carlos Henrique Miranda, Charles-Eric Durel, J.B. Royo, S. Roques, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universidad de Navarra [Pamplona] (UNAV), Institut d'Electronique du Solide et des Systèmes (InESS), Centre National de la Recherche Scientifique (CNRS), Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Conservatoire Végétal Régional d'Aquitaine, Partenaires INRAE, Conservatoire Vegetal Reg Aquitaine, F-47130 Dom Barolle, Montesquieu, France, and Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, Germplasm, Genetic diversity, microsatellite, [SDV]Life Sciences [q-bio], 04 agricultural and veterinary sciences, Horticulture, 01 natural sciences, SSR, identities, Geography, Malus × domestica, [SDE]Environmental Sciences, Gene duplication, 040103 agronomy & agriculture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 0401 agriculture, forestry, and fisheries, Microsatellite, Identification (biology), Cartography, Malus x domestica, 010606 plant biology & botany
Abstract

International audience; One of the possibilities to improve the management of germplasm collections is to identify the redundancies that inevitably appear within and between collections. For this purpose, an accurate identification of the preserved accessions is an indispensable requisite. In terms of identification, traditional methods based on morphological and agronomic traits are less effective than molecular markers due to the fact that they can be highly influenced by environmental factors. The aim of this study was to quantify the duplication degree among three apple collections located in the Spanish and French Pyrenean region, using a common set of 14 SSR markers, as well as to assess the genetic relationships between the accessions held in the three collections. Only 17 genotypes (approximate to 5% of the identified ones) were present in both Spanish and French collections. Two duplicates groups, nine (putative) synonyms and nine homonyms were identified. Remarkable differences in allelic variability and allelic frequencies distribution were found between the material preserved in Spanish and French collections, but the duplication and overlap highlighted the interest of coordinated international studies aiming at optimizing the management of germplasm collections.

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