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Genome-wide association mapping of flowering and ripening periods in apple

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dc.contributor.authorUrrestarazu Vidart, Jorge
dc.contributor.authorMuranty, Hélène
dc.contributor.authorDenancé, Caroline
dc.contributor.authorLeforestier, Diane
dc.contributor.authorRavon, Elisa
dc.contributor.authorGuyader, Arnaud
dc.contributor.authorGuisnel, Rémi
dc.contributor.authorFeugey, Laurence
dc.contributor.authorAubourg, Sébastien
dc.contributor.authorCelton, Jean Marc
dc.contributor.authorDaccord, Nicolas
dc.contributor.authorDondini, Luca
dc.contributor.authorGregori, Roberto
dc.contributor.authorLateur, Marc
dc.contributor.authorHouben, Patrick
dc.contributor.authorOrdidge, Matthew
dc.contributor.authorPaprstein, Frantisek
dc.contributor.authorSedlak, Jiri
dc.contributor.authorNybom, Hilde
dc.contributor.authorGarkava Gustavsson, Larisa
dc.contributor.authorTroggio, Michela
dc.contributor.authorBianco, Luca
dc.contributor.authorVelasco, Riccardo
dc.contributor.authorPoncet, Charles
dc.contributor.authorThéron, Anthony
dc.contributor.authorMoriya, Shigeki
dc.contributor.authorBink, Marco C. A. M.
dc.contributor.authorLaurens, François
dc.contributor.authorTartarini, Stefano
dc.contributor.authorDurel, Charles Eric
dc.contributor.departmentProducción Agrariaes_ES
dc.contributor.departmentNekazaritza Ekoizpenaeu
dc.date.accessioned2018-09-04T06:43:52Z
dc.date.available2018-09-04T06:43:52Z
dc.date.issued2017
dc.description.abstractDeciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.en
dc.description.sponsorshipJU has been partially supported by an Early Stage Research Fellowship of the Institute of Advanced Studies (University of Bologna).en
dc.format.extent19 p.
dc.format.mimetypeapplication/pdfen
dc.format.mimetypeapplication/zipen
dc.identifier.doi10.3389/fpls.2017.01923
dc.identifier.issn1664-462X (Electronic)
dc.identifier.urihttps://academica-e.unavarra.es/handle/2454/30446
dc.language.isoengen
dc.publisherFrontiers Mediaen
dc.relation.ispartofFrontiers in Plant Science, 8: 1923en
dc.relation.publisherversionhttps://doi.org/10.3389/fpls.2017.01923
dc.rights© 2017 Urrestarazu, Muranty, Denancé, Leforestier, Ravon, Guyader, Guisnel, Feugey, Aubourg, Celton, Daccord, Dondini, Gregori, Lateur, Houben, Ordidge, Paprstein, Sedlak, Nybom, Garkava-Gustavsson, Troggio, Bianco, Velasco, Poncet, Théron, Moriya, Bink, Laurens, Tartarini and Durel. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en
dc.rights.accessRightsinfo:eu-repo/semantics/openAccess
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/
dc.subjectAdaptive traitsen
dc.subjectAssociation geneticsen
dc.subjectGermplasm collectionen
dc.subjectGWAS, Malus × domestica Borkh.en
dc.subjectMicrosyntenyen
dc.subjectQuantitative trait locien
dc.subjectSNPen
dc.titleGenome-wide association mapping of flowering and ripening periods in appleen
dc.typeinfo:eu-repo/semantics/article
dc.type.versioninfo:eu-repo/semantics/publishedVersionen
dc.type.versionVersión publicada / Argitaratu den bertsioaes
dspace.entity.typePublication
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relation.isAuthorOfPublication.latestForDiscovery2d0a706d-1e23-4265-9157-d09e27cee0b9

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