Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 19, 2005
Publication Date: May 19, 2005
Citation: Snelling, W.M., Casas, E., Stone, R.T., Keele, J.W., Harhay, G.P., Bennett, G.L., Smith, T.P. 2005. Linkage mapping bovine EST-based SNP. Biomed Central (BMC) Genomics 6:74. Interpretive Summary: Nearly one thousand single nucleotide polymorphism (SNP) markers were developed and placed on a genetic map of cattle. The new markers are associated with genes, so the map with these markers indicates the position of some genes relative to anonymous DNA markers. Previous cattle maps were constructed primarily from anonymous DNA markers. Coupled with animal performance data and marker genotypes, these earlier maps are valuable to determine regions of the genome that may influence a particular trait, but provide little information about what genes are in a region and how they may affect performance. Incorporating the SNP gene markers provides limited information about genes an interesting region may contain, but these genes can be connected to well-described human and mouse genome sequences and maps to further illuminate genes in specific regions and how those genes might influence animal production.
Technical Abstract: Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC) sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. Chromosome assignment was determined for 862 of these SNP via twopoint linkage analyses; multipoint analyses established positions for 734 SNP. The bovine linkage map including these SNP represents 4964 markers on autosomes (no SNP were mapped on sex chromosomes), and 4888 markers on all chromosomes. The autosomal map includes 3689 microsatellites, 940 SNP and 65 other markers. The autosomal map contains markers in 2493 positions, with mean separation of 1.2 cM (maximum 9.1 cM) between marker positions. SNP appear in 595 positions, separated by a mean of 4.0 cM (maximum 59.3 cM). Confidence intervals for placement of all markers were estimated. Multi-allelic microsatellite markers had an average of 207 informative meioses, with a mean 3-lod confidence interval of 3.9 cM. The bi-allelic SNP averaged 49 informative meioses, and were placed within an average 8.5 cM 3-lod confidence interval. Addition of these bovine EST-based SNP to the linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. A cyclic map construction process allows the map to be updated easily, so that even after the bovine genome is completely sequenced, the map will continue to be a useful tool to connect observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits.