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Comparison of structure analyses and core collections for the management of walnut genetic resources

hal.structure.identifierBiologie du fruit et pathologie [BFP]
hal.structure.identifierCtifl - Centre de Lanxade [Ctifl - Centre de Lanxade ]
dc.contributor.authorBERNARD, Anthony
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBARRENECHE, Teresa
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDONKPEGAN, Armel
hal.structure.identifierCtifl - Centre de Lanxade [Ctifl - Centre de Lanxade ]
dc.contributor.authorLHEUREUX, Fabrice
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDIRLEWANGER, Elisabeth
dc.date.issued2020
dc.identifier.issn1614-2942
dc.description.abstractEnThe preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms ("maximum length subtree" and "entry-to-nearest-entry" methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management.
dc.language.isoen
dc.publisherSpringer Verlag
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectArbre fruitier
dc.subjectfruit à coque
dc.subjectnoyer
dc.subjectressource génétique
dc.subjectNoix
dc.subject.enCore collection
dc.subject.enWalnut
dc.subject.enGermplasm management
dc.subject.enSNP
dc.subject.enSSR
dc.title.enComparison of structure analyses and core collections for the management of walnut genetic resources
dc.typeArticle de revue
dc.identifier.doi10.1007/s11295-020-01469-5
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Amélioration des plantes
bordeaux.journalTree Genetics and Genomes
bordeaux.page76
bordeaux.volume16
bordeaux.issue5
bordeaux.peerReviewedoui
hal.identifierhal-02948538
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02948538v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Tree%20Genetics%20and%20Genomes&rft.date=2020&rft.volume=16&rft.issue=5&rft.spage=76&rft.epage=76&rft.eissn=1614-2942&rft.issn=1614-2942&rft.au=BERNARD,%20Anthony&BARRENECHE,%20Teresa&DONKPEGAN,%20Armel&LHEUREUX,%20Fabrice&DIRLEWANGER,%20Elisabeth&rft.genre=article


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