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Open Access Highly Accessed Open Badges Methodology article

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

Jean-Marc Celton1*, Alan Christoffels2, Daniel J Sargent3, Xiangming Xu3 and D Jasper G Rees14

Author Affiliations

1 Biotechnology Department, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa

2 South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa

3 East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK

4 Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa

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BMC Biology 2010, 8:155  doi:10.1186/1741-7007-8-155

Published: 30 December 2010



Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method.


The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps.


We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.