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Towards a joint international database: alignment of SSR marker data for european collections of cherry germplasm

hal.structure.identifierUniversity of Reading [UOR]
dc.contributor.authorORDIDGE, Matthew
hal.structure.identifierNational Institute of Agricultural Botany [NIAB]
dc.contributor.authorLITTHAUER, Suzanne
hal.structure.identifierUniversity of Reading [UOR]
dc.contributor.authorVENISON, Edward
hal.structure.identifierUnité Expérimentale Arboricole [UE ARBO]
dc.contributor.authorBLOUIN-DELMAS, Marine
hal.structure.identifierNational Institute of Agricultural Botany [NIAB]
dc.contributor.authorFERNANDEZ-FERNANDEZ, Felicidad
hal.structure.identifierJulius Kühn-Institut [JKI]
dc.contributor.authorHÖFER, Monika
hal.structure.identifierOffice Fédéral de l'Agriculture - Federal Office for Agriculture - Bundesamtes für Landwirtschaft [Berne] [OFAG]
dc.contributor.authorKÄGI, Christina
hal.structure.identifierAgroscope
dc.contributor.authorKELLERHALS, Markus
hal.structure.identifierUniversità degli studi di Palermo - University of Palermo
dc.contributor.authorMARCHESE, Annalisa
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorMARIETTE, Stéphanie
hal.structure.identifierSwedish University of Agricultural Sciences = Sveriges lantbruksuniversitet [SLU]
dc.contributor.authorNYBOM, Hilde
hal.structure.identifierResearch Centre on Food and Nutrition [CREA]
dc.contributor.authorGIOVANNINI, Daniela
dc.date.issued2021-06-18
dc.identifier.issn2223-7747
dc.description.abstractEnThe 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.
dc.language.isoen
dc.publisherMDPI
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enPrunus avium
dc.subject.ensweet cherry
dc.subject.enSSR
dc.subject.enmicrosatellite
dc.subject.engermplasm
dc.subject.engenetic resource
dc.title.enTowards a joint international database: alignment of SSR marker data for european collections of cherry germplasm
dc.typeArticle de revue
dc.identifier.doi10.3390/plants10061243
dc.subject.halSciences de l'environnement
bordeaux.journalPlants
bordeaux.page1-18
bordeaux.volume10
bordeaux.issue6
bordeaux.peerReviewedoui
hal.identifierhal-03280347
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03280347v1
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