Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Sep 23;14(9):19341-60.
doi: 10.3390/ijms140919341.

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

Aletta Bester-Van Der Merwe  1 , Sonja Blaauw, Jana Du Plessis, Rouvay Roodt-Wilding
Affiliations

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

Aletta Bester-Van Der Merwe et al. Int J Mol Sci. .

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 (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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Genoplots obtained with the GenomeStudio™ Genotyping Module representative of (a) a failed SNP; (b) a successfully genotyped (polymorphic) SNP; and (c) a monomorphic SNP analyzed in this study.
Figure 2
Figure 2
Factorial component analysis (FCA) based on 31 SNP loci in six H. midae populations. The respective populations are indicated by color: Family DS_1 (Yellow), Family DS_5 (Blue), Family DS_6 (White), Riet Point (Grey), Saldanha Bay (Pink) and Witsand (Green). The wild populations are encircled.
See this image and copyright information in PMC

References

    1. An H.S., Lee J.W., Kim H.C., Myeong J.-I. Genetic characterization of five hatchery populations of the pacific abalone (Haliotis discus hannai) using microsatellite markers. Int. J. Mol. Sci. 2011;12:4836–4849. - PMC - PubMed
    1. Department of Agriculture Forestry and Fisheries Aquaculture Annual Report 2011 March 2012, 15.Available online: http://www.nda.agric.za/doaDev/fisheries/(accessed on 17 June 2013)
    1. Rhode C., Hepple J., Jansen S., Davis T., Vervalle J., Bester-van der Merwe A.E., Roodt-Wilding R. A Population genetic analysis of abalone domestication events in South Africa: Implications for the management of the abalone resource. Aquaculture. 2012;356:235–242.
    1. Bester A.E., Slabbert R., D’Amato M.E. Isolation and characterisation of microsatellite markers in the South African abalone (Haliotis midae) Mol. Ecol. Resour. 2004;4:618–619.
    1. Slabbert R., Ruivo N.R., Van den Berg N.C., Lizamore D.L., Roodt-Wilding R. Isolation and characterisation of 63 microsatellite loci for the abalone Haliotis midae. J. World Aquacult. Soc. 2008;39:429–435.

Publication types

LinkOut - more resources