High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

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dc.contributor.authorUncu, Ayse Ozgur
dc.contributor.authorUncu, Ali Tevfik
dc.date.accessioned2024-02-23T14:20:31Z
dc.date.available2024-02-23T14:20:31Z
dc.date.issued2020
dc.departmentNEÜen_US
dc.description.abstractCarrot (Daucus carota L.) is a versatile vegetable crop and the most economically important member of the Apiaceae family. While there are several important cultivated species in the family such as celery, parsley, cumin, fennel, coriander and parsnip, molecular genetic research in Apiaceae is relatively limited compared to other agriculturally important taxa. In the present work, an in silico approach was employed in order to develop chromosome-anchored simple sequence repeat (SSR) markers from the carrot genome assembly. A total of 55,386 markers were developed and marker loci that correspond to protein coding sequences were determined. In silico mapping analysis predicted that 51,160 of these were single-locus markers and 4,226 amplified more than one locus. Cross-species transferability of the markers was assessed using the fennel (Foeniculum vulgare Mill.) draft genome sequence, resulting in the identification of 578 low-copy transferable markers. These markers can serve for the purposes of interspecific genomic synteny studies and comparative gene identification/cloning. A subset of 50 markers was evaluated on DNA from 17 accessions of carrot. As a result, 46 (92%) produced amplicons from all genotypes, of which 28 (61%) displayed polymorphisms among the 17 carrot accessions, confirming the potential of the newly developed markers to reveal genotypic diversity in cultivated carrot. With the present work, carrot chromosomes were saturated with sequence-specific markers, which constitute a physical map of the carrot genome. The collection of markers will serve as practical molecular tools for germplasm characterization, gene tagging and molecular breeding studies in this important crop species.en_US
dc.identifier.doi10.1080/13102818.2019.1701551
dc.identifier.endpage9en_US
dc.identifier.issn1310-2818
dc.identifier.issn1314-3530
dc.identifier.issue1en_US
dc.identifier.scopus2-s2.0-85076412740en_US
dc.identifier.scopusqualityQ3en_US
dc.identifier.startpage1en_US
dc.identifier.urihttps://doi.org/10.1080/13102818.2019.1701551
dc.identifier.urihttps://hdl.handle.net/20.500.12452/13195
dc.identifier.volume34en_US
dc.identifier.wosWOS:000595211800001en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherTaylor & Francis Ltden_US
dc.relation.ispartofBiotechnology & Biotechnological Equipmenten_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectApiaceaeen_US
dc.subjectDna Markersen_US
dc.subjectMicrosatellitesen_US
dc.subjectMolecular Breedingen_US
dc.subjectUmbelliferaeen_US
dc.titleHigh-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markersen_US
dc.typeArticleen_US

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