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Updated: Jun 5, 2026
13:33
Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly
Jean-Marc Celton1, Alan Christoffels, Daniel J Sargent
1Biotechnology Department, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa. jean-marc.celton@angers.inra.fr
BMC Biology
|January 4, 2011
Summary
A new whole genome single nucleotide polymorphism sequencing strategy positions genome sequence contigs onto genetic linkage maps. This method successfully anchored most sequence assemblies for Venturia inaequalis and Fragaria vesca.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Genome assembly contigs and scaffolds require precise positioning within an organism's genome.
- Current sequencing projects face challenges in accurately ordering and orienting assembled genomic sequences.
Purpose of the Study:
- To develop and validate a novel strategy for whole genome sequencing.
- To enable the positioning of sequence contigs onto genetic linkage maps using bin mapping.
Main Methods:
- Whole genome single nucleotide polymorphism (SNP) sequencing strategy.
- Bin mapping method for anchoring sequence contigs to linkage maps.
- Application to draft genomes of Venturia inaequalis and Fragaria vesca.
Main Results:
- Successfully anchored 70% of sequence assemblies for Venturia inaequalis.
- Achieved 92% anchoring of sequence assemblies for Fragaria vesca.
- Demonstrated accurate bin map positioning for the majority of large sequence contigs.
Conclusions:
- The developed SNP sequencing strategy effectively positions genome sequence contigs.
- The method was validated by mapping single sequence repeat markers on a full population.
- This approach enhances the utility of genome assemblies in various sequencing projects.
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