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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application
Aletta Bester-Van Der Merwe1, Sonja Blaauw, Jana Du Plessis
1Molecular Breeding and Biodiversity Group, Department of Genetics, Faculty of Agrisciences, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa. aeb@sun.ac.za.
International Journal of Molecular Sciences
|September 26, 2013
Summary
This study identifies and validates single nucleotide polymorphisms (SNPs) in Haliotis midae, crucial molecular markers for genetic management and aquaculture improvement of this vulnerable abalone species.
Area of Science:
- Aquaculture
- Genomics
- Marine Biology
Background:
- Haliotis midae is a commercially valuable but vulnerable abalone species.
- Genetic management is essential for preserving wild and cultured stocks.
- Molecular markers like single nucleotide polymorphisms (SNPs) are vital for genetic improvement.
Purpose of the Study:
- To identify and validate single nucleotide polymorphisms (SNPs) in Haliotis midae.
- To assess the utility of these SNPs for population structure analysis and linkage map construction.
- To explore the application of SNPs in marker-assisted selection for abalone aquaculture.
Main Methods:
- Transcriptome sequences were used for in silico identification of 505 putative SNPs.
- A subset of 234 SNPs was validated using Illumina GoldenGate genotyping assays and VeraCode technology.
- Population structure analysis and linkage map construction potential were assessed.
Main Results:
- 505 putative SNPs were identified, with 234 validated.
- The genotyping platform showed a 65%-69% conversion rate and 76%-85% success rate.
- 31 validated SNPs were useful for population structure analysis, and 174 are candidates for linkage map construction.
Conclusions:
- SNP validation in Haliotis midae is feasible using high-throughput genotyping.
- Validated SNPs are valuable for population genetics, linkage mapping, and marker-assisted selection in abalone aquaculture.
- This research provides essential genetic tools for the conservation and improvement of Haliotis midae.
Related Concept Videos
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...