Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

dc.contributor.authorCelton, Jean M.
dc.contributor.authorChristoffels, Alan
dc.contributor.authorSargant, Daniel J.
dc.contributor.authorXu, Xiangming
dc.contributor.authorRees, Jasper G.
dc.date.accessioned2015-06-22T14:29:53Z
dc.date.available2015-06-22T14:29:53Z
dc.date.issued2010
dc.description.abstractDetermining the position and order of contigs and scaffolds from a genome assembly within an organism’s genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing. We developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.en_US
dc.description.accreditationWeb of Science
dc.description.sponsorshipDeciduous Fruit Producers Trust THRIP Program National Research Foundation Claude Harris Leon Foundationen_US
dc.identifier.citationCelton et al.: Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biology 2010 8:155.en_US
dc.identifier.issn1741-7007
dc.identifier.urihttp://hdl.handle.net/10566/1525
dc.language.isoenen_US
dc.privacy.showsubmitterfalse
dc.publisherBioMed Central
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttp://dx.doi.org/10.1186/1741-7007-8-155
dc.status.ispeerreviewedtrue
dc.subjectWhole genome analysisen_US
dc.subjectSingle nucleotide polymorphism (SNP)en_US
dc.subjectBin mapping methoden_US
dc.titleGenome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage mapen_US
dc.typeArticleen_US

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