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Ordidge M, Litthauer S, Venison E, Blouin-Delmas M, Fernandez-Fernandez F, Höfer M, Kägi C, Kellerhals M, Marchese A, Mariette S, Nybom H, Giovannini D. Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm. Plants (Basel) 2021; 10:1243. [PMID: 34207415 PMCID: PMC8235247 DOI: 10.3390/plants10061243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022]
Abstract
The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.
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Affiliation(s)
- Matthew Ordidge
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Suzanne Litthauer
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK; (S.L.); (F.F.-F.)
| | - Edward Venison
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Marine Blouin-Delmas
- INRAE-Unité Expérimentale Arboricole, Domaine de la Tour de Rance, 47320 Bourran, France;
| | | | - Monika Höfer
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn Institute, Pillnitzer Platz 3a, 01326 Dresden, Germany;
| | - Christina Kägi
- Federal Office for Agriculture, Genetic Resources and Technologies, Schwarzenburgstrasse 165, 3003 Bern, Switzerland;
| | - Markus Kellerhals
- Agroscope, Strategic Research Division Plant Breeding, Müller-Thurgau-Str. 29, 8820 Wädenswil, Switzerland;
| | - Annalisa Marchese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze-Ed. 4, 90128 Palermo, Italy;
| | - Stephanie Mariette
- BIOGECO, INRAE, University of Bordeaux, Route d’Arcachon 69, 33612 Cestas, France;
| | - Hilde Nybom
- Balsgård-Department of Plant Breeding, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
| | - Daniela Giovannini
- CREA-Research Centre for Olive, Fruit and Citrus Crops, via la Canapona 1 bis, 47121 Forlì, Italy;
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Urrestarazu J, Denancé C, Ravon E, Guyader A, Guisnel R, Feugey L, Poncet C, Lateur M, Houben P, Ordidge M, Fernandez-Fernandez F, Evans KM, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Miranda C, Gassmann J, Kellerhals M, Suprun I, Pikunova AV, Krasova NG, Torutaeva E, Dondini L, Tartarini S, Laurens F, Durel CE. 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 Biol 2016; 16:130. [PMID: 27277533 PMCID: PMC4898379 DOI: 10.1186/s12870-016-0818-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 05/18/2023]
Abstract
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.
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Affiliation(s)
- Jorge Urrestarazu
- 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
| | - Caroline Denancé
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Elisa Ravon
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Arnaud Guyader
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Rémi Guisnel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Laurence Feugey
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles Poncet
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
| | - Marc Lateur
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Patrick Houben
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | | | - Kate M Evans
- Washington State University Tree Fruit Research and Extension Center, 1100 N Western Ave, Wenatchee, WA, 98801, USA
| | - Frantisek Paprstein
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Jiri Sedlak
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Fjälkestadsvägen 459, Swedish University of Agricultural Sciences, 291 94, Kristianstad, Sweden
| | - Larisa Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden
| | - Carlos Miranda
- Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain
| | - Jennifer Gassmann
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Markus Kellerhals
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Ivan Suprun
- NCRRIH&V, North Caucasian Regional Research Institute of Horticulture and Viticulture, 39, 40-letiya Pobedy street, Krasnodar, 350901, Russian Federation
| | - Anna V Pikunova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Nina G Krasova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Elnura Torutaeva
- Kyrgyz National Agrarian University, 68 Mederova Street, 720005, Bishkek, Kyrgyzstan
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - François Laurens
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles-Eric Durel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
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