Transcriptome-wide single nucleotide polymorphisms (SNPs) for Abalone (Haliotis midae) : validation and application using GoldenGate medium-throughput genotyping assays

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dc.contributor.authorBester-Van der Merwe, Alettaen_ZA
dc.contributor.authorBlaauw, Sonjaen_ZA
dc.contributor.authorDu Plessis, Janaen_ZA
dc.contributor.authorRoodt-Wilding, Rouvayen_ZA
dc.date.accessioned2014-02-13T14:22:16Z
dc.date.available2014-02-13T14:22:16Z
dc.date.issued2013-09
dc.descriptionPublication of this article was funded by the Stellenbosch University Open Access Fund.en_ZA
dc.descriptionThe original publication is available at http://www.mdpi.com/journal/ijmsen_ZA
dc.description.abstractHaliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular markers, such as microsatellites and single nucleotide (SNPs). Transcriptome sequences generated through sequencing-by-synthesis technology were utilized for the in vitro and in silico identification of 505 putative SNPs from a total of 316 selected contigs. A subset of 234 SNPs were further validated and characterized in wild and cultured abalone using two Illumina GoldenGate genotyping assays. Combined with VeraCode technology, this genotyping platform yielded a 65%−69% conversion rate (percentage polymorphic markers) with a global genotyping success rate of 76%−85% and provided a viable means for validating SNP markers in a non-model species. The utility of 31 of the validated SNPs in population structure analysis was confirmed, while a large number of SNPs (174) were shown to be informative and are, thus, good candidates for linkage map construction. The non-synonymous SNPs (50) located in coding regions of genes that showed similarities with known proteins will also be useful for genetic applications, such as the marker-assisted selection of genes of relevance to abalone aquaculture.en_ZA
dc.description.sponsorshipStellenbosch Universityen_ZA
dc.description.versionPublishers' versionen_ZA
dc.format.extentp. 19341-19360 : ill.
dc.identifier.citationBester-Van der Merwe, A., Blaauw, S., Du Plessis, J. & Roodt-Wilding, R. 2013. Transcriptome-wide single nucleotide polymorphisms (SNPs) for Abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays. International Journal of Molecular Sciences,14:19341-19360, doi:10.3390/ijms140919341.en_ZA
dc.identifier.issn1422-0067 (print)
dc.identifier.issn1422-0067 (online)
dc.identifier.otherdoi:10.3390/ijms140919341
dc.identifier.urihttp://hdl.handle.net/10019.1/86144
dc.language.isoen_ZAen_ZA
dc.publisherMDPIen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectHaliotis midae (abalone) -- Geneticsen_ZA
dc.subjectSNP (single nucleotide polymorphisms) validationen_ZA
dc.subjectMedium-throughput genotypingen_ZA
dc.titleTranscriptome-wide single nucleotide polymorphisms (SNPs) for Abalone (Haliotis midae) : validation and application using GoldenGate medium-throughput genotyping assaysen_ZA
dc.typeArticleen_ZA
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