Submitted to: Mammalian Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2001
Publication Date: 2/2/2002
Citation: Stone, R.T., Grosse, W., Casas, E., Smith, T.P., Keele, J.W., Bennett, G.L. 2002. Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mammalian Genome. 13:211-215.
Interpretive Summary: The bovine genetic linkage map was constructed with microsatellites serving as markers. Unfortunately, microsatellites are largely species-specific markers which don't allow comparisons with the more complete gene-based genetic maps in humans and model organisms. Over the last two years, several research groups have obtained and made public partial sequences of bovine genes referred to as expressed sequence tags or ESTs. We are reporting our initial efforts to place ESTs on the bovine linkage map. Our approach is to use the partial gene sequences to sequence parents in mapping families. Frequently, these animal sequences differ at a single base which has been termed single nucleotide polymorphism (SNP). Thus, genotyping an SNP in a mapping family places a gene or EST on the linkage map. This permits the comparison of the bovine map to gene-based maps in other species. Or in essence, a gene-based map in cattle is the gateway into the extensive genetic data on gene order and function in other organisms. Besides providing evidence that our approach of genotyping SNPs is viable, the SNPs discovered provide a set of nonmicrosatellite markers for additional genetic studies utilizing high throughput genotyping technology.
Technical Abstract: Single nucleotide polymorphisms (SNP) developed from 50 bovine expressed sequence tags (ESTs) have been mapped into the existing bovine linkage map. Primers for generating sequence tag sites (STSs) for SNP discovery in the sires from the U.S. MARC reference families were restricted to ESTs with sufficient homology to human genomic sequence to predict intron-exon boundaries. A primer extension/mass spectrometry genotyping assay was developed for a single SNP corresponding to each EST and the informative families were genotyped using the Sequenom MassArray system. This genotyping approach proved to be robust for genotyping accuracy and optimization of individual assays was minimal. Considering only ESTs with matching human sequence resulted in 92% of the 50 ESTs being orthologous to human UniGene clusters or GenBank sequence. Also, 20 of the ESTs mapped had human orthologs in four regions where extensive sequence has been completed. Only one EST mapped to a chromosome not predicted by conserved synteny between bovine and human maps. We have demonstrated the feasability of constructing a linkage map based on SNPs associated with ESTs. This will improve upon existing comparative mapping data and provide the basics for developing an SNP-based map suitable for genomic scans that utilize technology being developed for high throughput SNP genotyping.