Journal article
Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level.
- Urrestarazu J IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
- Denancé C IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
- Ravon E IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
- Guyader A IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
- Guisnel R IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
- Feugey L IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
- Poncet C Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France.
- Lateur M CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium.
- Houben P CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium.
- Ordidge M School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK.
- Fernandez-Fernandez F NIAB EMR, East Malling Research, East Malling, Kent, ME19 6BJ, United Kingdom.
- Evans KM Washington State University Tree Fruit Research and Extension Center, 1100 N Western Ave, Wenatchee, WA, 98801, USA.
- Paprstein F RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic.
- Sedlak J RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic.
- Nybom H Department of Plant Breeding, Balsgård, Fjälkestadsvägen 459, Swedish University of Agricultural Sciences, 291 94, Kristianstad, Sweden.
- Garkava-Gustavsson L Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden.
- Miranda C Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain.
- Gassmann J Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland.
- Kellerhals M Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland.
- Suprun I NCRRIH&V, North Caucasian Regional Research Institute of Horticulture and Viticulture, 39, 40-letiya Pobedy street, Krasnodar, 350901, Russian Federation.
- Pikunova AV VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation.
- Krasova NG VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation.
- Torutaeva E Kyrgyz National Agrarian University, 68 Mederova Street, 720005, Bishkek, Kyrgyzstan.
- Dondini L Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy.
- Tartarini S Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy.
- Laurens F IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
- Durel CE IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France. charles-eric.durel@angers.inra.fr.
- 2016-06-10
Published in:
- BMC plant biology. - 2016
Differentiation
Genetic resources
Malus x domestica Borkh.
Parentage analysis
Population structure
SSR markers
Variability
Europe
Gene Flow
Genetic Markers
Genetic Variation
Genome-Wide Association Study
Genotype
Malus
Microsatellite Repeats
Phylogeny
English
BACKGROUND
The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.
RESULTS
A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.
CONCLUSIONS
The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.
RESULTS
A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.
CONCLUSIONS
The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
- Language
-
- English
- Open access status
- gold
- Identifiers
-
- DOI 10.1186/s12870-016-0818-0
- PMID 27277533
- Persistent URL
- https://folia.unifr.ch/global/documents/146053
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