Afficher la notice abrégée

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

hal.structure.identifierUnited States Department of Agriculture [USDA]
dc.contributor.authorBASSIL, Nahla V.
hal.structure.identifierUniversity of New Hampshire [UNH]
dc.contributor.authorDAVIS, Thomas M.
hal.structure.identifierUniversity of New Hampshire [UNH]
dc.contributor.authorZHANG, Hailong
hal.structure.identifierWashington State University [WSU]
dc.contributor.authorFICKLIN, Stephen
hal.structure.identifierAffymetrix Inc.
dc.contributor.authorMITTMANN, Mike
hal.structure.identifierAffymetrix Inc.
dc.contributor.authorWEBSTER, Teresa
hal.structure.identifierUniversity of New Hampshire [UNH]
dc.contributor.authorMAHONEY, Lise L.
hal.structure.identifierUniversity of New Hampshire [UNH]
dc.contributor.authorWOOD, David
hal.structure.identifierUnited States Department of Agriculture [USDA]
dc.contributor.authorALPERIN, Elisabeth S.
hal.structure.identifierMichigan State University [East Lansing]
dc.contributor.authorROSYARA, Umesh R.
hal.structure.identifierWageningen University and Research [Wageningen] [WUR]
dc.contributor.authorKOEHORST-VANC PUTTEN, Herma
hal.structure.identifierInstitut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology [IRTA]
dc.contributor.authorMONFORT, Amparo
hal.structure.identifierFondazione Edmund Mach
dc.contributor.authorSARGENT, Daniel J.
hal.structure.identifierInstituto Andaluz de Investigación y Formación Agraria y Pesquera [IFAPA]
dc.contributor.authorAMAYA, Iraida
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDENOYES, Beatrice
hal.structure.identifierFondazione Edmund Mach
dc.contributor.authorBIANCO, Luca
hal.structure.identifierWageningen University and Research [Wageningen] [WUR]
dc.contributor.authorVAN DIJK, Thijs
hal.structure.identifierAffymetrix Inc.
dc.contributor.authorPIRANI, Ali
hal.structure.identifierMichigan State University [East Lansing]
dc.contributor.authorIEZZONI, Amy
hal.structure.identifierWashington State University [WSU]
dc.contributor.authorMAIN, Dorrie
hal.structure.identifierWashington State University [WSU]
dc.contributor.authorPEACE, Cameron
hal.structure.identifierUniversity of New Hampshire [UNH]
dc.contributor.authorYANG, Yilong
hal.structure.identifierUniversity of Florida [Gainesville] [UF]
dc.contributor.authorWHITAKER, Vance M.
hal.structure.identifierUniversity of Florida [Gainesville] [UF]
dc.contributor.authorVERMA, Sujeet
hal.structure.identifierAffymetrix UK Ltd
dc.contributor.authorBELLON, Laurent
hal.structure.identifierAffymetrix UK Ltd
dc.contributor.authorBREW, Fiona
hal.structure.identifierUniversidad de Talca
dc.contributor.authorHERRERA, Raul
hal.structure.identifierWageningen University and Research [Wageningen] [WUR]
dc.contributor.authorVAN DE WEG, Eric
dc.date.issued2015
dc.identifier.issn1471-2164
dc.description.abstractEn<strong>Background</strong> A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. <strong>Results</strong> About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. <strong>Conclusions</strong> The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
dc.language.isoen
dc.publisherBioMed Central
dc.subject.enfragaria
dc.subject.engenotyping array
dc.subject.enplant breeding
dc.subject.enpolyploidy
dc.subject.enstrawberry
dc.subject.eningle nucleotide polymorphism
dc.subject.enreduced ploidy
dc.title.enDevelopment and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
dc.typeArticle de revue
dc.identifier.doi10.1186/s12864-015-1310-1
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.journalBMC Genomics
bordeaux.page30 p.
bordeaux.volume16
bordeaux.peerReviewedoui
hal.identifierhal-02639308
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02639308v1
bordeaux.COinSctx_ver=Z39.88-2004&amp;rft_val_fmt=info:ofi/fmt:kev:mtx:journal&amp;rft.jtitle=BMC%20Genomics&amp;rft.date=2015&amp;rft.volume=16&amp;rft.spage=30%20p.&amp;rft.epage=30%20p.&amp;rft.eissn=1471-2164&amp;rft.issn=1471-2164&amp;rft.au=BASSIL,%20Nahla%20V.&amp;DAVIS,%20Thomas%20M.&amp;ZHANG,%20Hailong&amp;FICKLIN,%20Stephen&amp;MITTMANN,%20Mike&amp;rft.genre=article


Fichier(s) constituant ce document

FichiersTailleFormatVue

Il n'y a pas de fichiers associés à ce document.

Ce document figure dans la(les) collection(s) suivante(s)

Afficher la notice abrégée