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

BMC Plant Biology

Research Article

Jennifer Gassmann¹  Markus Kellerhals¹  Marc Lateur²  Patrick Houben²  Luca Dondini³  Stefano Tartarini³  Hilde Nybom⁴  Larisa Garkava-Gustavsson⁵  Caroline Denancé⁶  François Laurens⁶  Arnaud Guyader⁶  Elisa Ravon⁶  Laurence Feugey⁶  Charles-Eric Durel⁶  Rémi Guisnel⁶  Jorge Urrestarazu⁷  Elnura Torutaeva⁸  Ivan Suprun⁹  Felicidad Fernandez-Fernandez^1,10  Charles Poncet^1,11  Carlos Miranda^1,12  Frantisek Paprstein^1,13  Jiri Sedlak^1,13  Matthew Ordidge^1,14  Anna V. Pikunova^1,15  Nina G. Krasova^1,15  Kate M. Evans^1,16 

[1] Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland;CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium;Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy;Department of Plant Breeding, Balsgård, Fjälkestadsvägen 459, Swedish University of Agricultural Sciences, 291 94, Kristianstad, Sweden;Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden;IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France;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;Kyrgyz National Agrarian University, 68 Mederova Street, 720005, Bishkek, Kyrgyzstan;NCRRIH&V, North Caucasian Regional Research Institute of Horticulture and Viticulture, 39, 40-letiya Pobedy street, 350901, Krasnodar, Russian Federation;NIAB EMR, East Malling Research, East Malling, ME19 6BJ, Kent, United Kingdom;Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France;Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain;RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic;School of Agriculture, Policy and Development, University of Reading, Whiteknights, RG6 6AR, Reading, UK;VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation;Washington State University Tree Fruit Research and Extension Center, 1100 N Western Ave, 98801, Wenatchee, WA, USA;

关键词: Malus;    Genetic resources;    Population structure;    Variability;    SSR markers;    Differentiation;    Parentage analysis;   

DOI  :  10.1186/s12870-016-0818-0

 received in 2016-02-23, accepted in 2016-05-23,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsA 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2016