Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level.
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.



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.



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.
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.|Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy.|Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain.
Jorge
J
Urrestarazu
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
Caroline
C
Denancé
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
Elisa
E
Ravon
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
Arnaud
A
Guyader
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
Rémi
R
Guisnel
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
Laurence
L
Feugey
Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France.
Charles
C
Poncet
CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium.
Marc
M
Lateur
CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium.
Patrick
P
Houben
School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK.
Matthew
M
Ordidge
NIAB EMR, East Malling Research, East Malling, Kent, ME19 6BJ, United Kingdom.
Felicidad
F
Fernandez-Fernandez
Washington State University Tree Fruit Research and Extension Center, 1100 N Western Ave, Wenatchee, WA, 98801, USA.
Kate M
KM
Evans
RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic.
Frantisek
F
Paprstein
RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic.
Jiri
J
Sedlak
Department of Plant Breeding, Balsgård, Fjälkestadsvägen 459, Swedish University of Agricultural Sciences, 291 94, Kristianstad, Sweden.
Hilde
H
Nybom
Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden.
Larisa
L
Garkava-Gustavsson
Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain.
Carlos
C
Miranda
Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland.
Jennifer
J
Gassmann
Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland.
Markus
M
Kellerhals
NCRRIH&V, North Caucasian Regional Research Institute of Horticulture and Viticulture, 39, 40-letiya Pobedy street, Krasnodar, 350901, Russian Federation.
Ivan
I
Suprun
VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation.
Anna V
AV
Pikunova
VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation.
Nina G
NG
Krasova
Kyrgyz National Agrarian University, 68 Mederova Street, 720005, Bishkek, Kyrgyzstan.
Elnura
E
Torutaeva
Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy.
Luca
L
Dondini
Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy.
Stefano
S
Tartarini
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
François
F
Laurens
IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France. charles-eric.durel@angers.inra.fr.
Charles-Eric
CE
Durel
D005060:Europe; D051456:Gene Flow; D005819:Genetic Markers; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D027845:Malus / Q000145:classification / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D018895:Microsatellite Repeats; D010802:Phylogeny
D005819:Genetic Markers
Differentiation; Genetic resources; Malus x domestica Borkh.; Parentage analysis; Population structure; SSR markers; Variability