Int. J. Mol. Sci. 2013, 14(9), 19341-19360; doi:10.3390/ijms140919341
Article

Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

Molecular Breeding and Biodiversity Group, Department of Genetics, Faculty of Agrisciences, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
* Author to whom correspondence should be addressed.
Received: 26 July 2013; in revised form: 26 August 2013 / Accepted: 5 September 2013 / Published: 23 September 2013
(This article belongs to the Section Molecular Diagnostics)
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Abstract: Haliotis 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 Polymorphisms (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.
Keywords: abalone; Haliotis midae; SNP validation; transcriptome; GoldenGate assay; medium-throughput genotyping

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MDPI and ACS Style

Bester-Van Der Merwe, A.; Blaauw, S.; Du Plessis, J.; Roodt-Wilding, R. Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays. Int. J. Mol. Sci. 2013, 14, 19341-19360.

AMA Style

Bester-Van Der Merwe A, Blaauw S, Du Plessis J, Roodt-Wilding R. Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays. International Journal of Molecular Sciences. 2013; 14(9):19341-19360.

Chicago/Turabian Style

Bester-Van Der Merwe, Aletta; Blaauw, Sonja; Du Plessis, Jana; Roodt-Wilding, Rouvay. 2013. "Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs) for Abalone (Haliotis midae): Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays." Int. J. Mol. Sci. 14, no. 9: 19341-19360.

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