SNP discovery by GBS in olive and the construction of a high-density genetic linkage map

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dc.contributor.authorTangu, Nesrin Aktepe
dc.contributor.authorÖz, Ayşe Tülin
dc.contributor.buuauthorİpek, Ahmet
dc.contributor.buuauthorYılmaz, Kübra
dc.contributor.buuauthorSıkıcı, Pelin
dc.contributor.buuauthorBayraktar, Murat
dc.contributor.buuauthorİpek, Meryem
dc.contributor.buuauthorGülen, Hatice
dc.contributor.departmentUludağ Üniversitesi/Ziraat Fakültesi/Bahçe Bitkileri Bölümü.tr_TR
dc.contributor.departmentUludağ Üniversitesi/Fen-Edebiyat Fakültesi/Moleküler Biyoloji ve Genetik Bölümü.tr_TR
dc.contributor.orcid0000-0001-7586-3108tr_TR
dc.contributor.researcheridAAH-3233-2021tr_TR
dc.contributor.researcheridAFW-5375-2022tr_TR
dc.contributor.scopusid6603912487tr_TR
dc.contributor.scopusid57194530243tr_TR
dc.contributor.scopusid57140804800tr_TR
dc.contributor.scopusid57140106700tr_TR
dc.contributor.scopusid16031208900tr_TR
dc.contributor.scopusid6603211102tr_TR
dc.date.accessioned2022-05-20T07:02:04Z
dc.date.available2022-05-20T07:02:04Z
dc.date.issued2016-06
dc.description.abstractGenetic linkage maps are valuable tools for genetic, genomic, and crop breeding studies. Several genetic linkage maps were constructed for the olive (Olea europaea L.) genome, mainly using amplified fragment length polymorphisms (AFLPs) and simple sequence repeat (SSR) markers. However, AFLPs and SSR markers were not enough to develop a high-density olive linkage map. Genotyping-by-sequencing (GBS), a recently developed single-nucleotide polymorphism (SNP) identification methodology based on next-generation sequencing (NGS) technologies, has been demonstrated to be useful for the identification of a high number of SNP markers and the construction of high-density genetic linkage maps. In the present study, we identified a total of 10,941 SNPs from a cross between the olive cultivars 'Gemlik' and 'Edincik Su' using GBS and de novo SNP discovery implemented in the computer program "Stacks." A high-density genetic linkage map for the olive genome was constructed using 121 cross-pollinated full-sib F1 progeny and 5643 markers (21 SSRs, 203 AFLPs, and 5736 SNPs). This linkage map was composed of 25 linkage groups, covering 3049 cM of the olive genome, and the mean distance between the flanking markers was 0.53 cM. To the best of our knowledge, this map is the most saturated genetic linkage map in olive to date. We demonstrated that GBS is a valuable tool for the identification of thousands of SNPs for the construction of a saturated genetic linkage map in olive. The high-density genetic map developed in this study is a useful tool for locating quantitative trait loci and other economically important traits in the olive genome.en_US
dc.identifier.citationİpek, A. vd. (2016). "SNP discovery by GBS in olive and the construction of a high-density genetic linkage map". Biochemical Genetics, 54(3), 313-325.en_US
dc.identifier.endpage325tr_TR
dc.identifier.issn0006-2928
dc.identifier.issn1573-4927
dc.identifier.issue3tr_TR
dc.identifier.pubmed26902470tr_TR
dc.identifier.scopus2-s2.0-84959126642tr_TR
dc.identifier.startpage313tr_TR
dc.identifier.urihttps://doi.org/10.1007/s10528-016-9721-5
dc.identifier.urihttps://link.springer.com/article/10.1007/s10528-016-9721-5
dc.identifier.urihttp://hdl.handle.net/11452/26542
dc.identifier.volume54tr_TR
dc.identifier.wos000376983400010tr_TR
dc.indexed.pubmedPubMeden_US
dc.indexed.scopusScopusen_US
dc.indexed.wosSCIEen_US
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.relation.bapOUAP(Z)-2013/33en_US
dc.relation.collaborationYurt içitr_TR
dc.relation.collaborationSanayitr_TR
dc.relation.journalBiochemical Geneticsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergitr_TR
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectBiochemistry & molecular biologyen_US
dc.subjectGenetics & heredityen_US
dc.subjectGBSen_US
dc.subjectGenetic mappingen_US
dc.subjectOlea europaea L.en_US
dc.subjectOliveen_US
dc.subjectSNP discoveryen_US
dc.subjectMarkersen_US
dc.subjectCultivarsen_US
dc.subjectGenomeen_US
dc.subjectPopulationsen_US
dc.subjectDiversityen_US
dc.subjectGermplasmen_US
dc.subjectSequencesen_US
dc.subjectAflpen_US
dc.subject.emtreeAmplified fragment length polymorphismen_US
dc.subject.emtreeComputer programen_US
dc.subject.emtreeCultivaren_US
dc.subject.emtreeGene frequencyen_US
dc.subject.emtreeGene mutationen_US
dc.subject.emtreeGenetic linkageen_US
dc.subject.emtreeGenetic markeren_US
dc.subject.emtreeGenetic polymorphismen_US
dc.subject.emtreeGenotypeen_US
dc.subject.emtreeNext generation sequencingen_US
dc.subject.emtreeOliveen_US
dc.subject.emtreeProgenyen_US
dc.subject.emtreeQuantitative trait locusen_US
dc.subject.emtreeSimple sequence repeaten_US
dc.subject.emtreeSingle nucleotide polymorphismen_US
dc.subject.emtreeChromosomal mappingen_US
dc.subject.emtreeGenetic linkageen_US
dc.subject.emtreeGeneticsen_US
dc.subject.emtreeGrowth, development and agingen_US
dc.subject.emtreeHigh throughput sequencingen_US
dc.subject.emtreeOlive treeen_US
dc.subject.emtreePlant genomeen_US
dc.subject.emtreeProceduresen_US
dc.subject.meshChromosome mappingen_US
dc.subject.meshGenetic linkageen_US
dc.subject.meshGenome, planten_US
dc.subject.meshHigh-throughput nucleotide sequencingen_US
dc.subject.meshOleaen_US
dc.subject.meshPolymorphism, single nucleotideen_US
dc.subject.meshQuantitative trait locien_US
dc.subject.scopusOlea; Hedgerow; Genetic Variabilityen_US
dc.subject.wosBiochemistry & molecular biologyen_US
dc.subject.wosGenetics & heredityen_US
dc.titleSNP discovery by GBS in olive and the construction of a high-density genetic linkage mapen_US
dc.typeArticle

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