Skip to main content Accessibility help

Population parameters incorporated into genome-wide tagSNP selection

  • A. P. Silesian (a1) and J. Szyda (a1)
  • Please note a correction has been issued for this article.

Single nucleotide polymorphisms (SNPs) are the most widespread source of variation in genomes. While the very large number of SNPs allows for a very precise description of genetic variation, it impedes data processing and significantly increases analysis time. Many of the SNPs located close to each other frequently carry the same or similar information. This problem can be solved by selecting the most informative SNPs (tagSNPs) using linkage disequilibrium information by identifying a set of tagSNPs representative for a chromosome fragment. The goal of this study is to check whether the genetic structure of a population, expressed by relationship and inbreeding coefficients, affects tagSNP selection. Six subsets of 450 bulls are selected out of the 1228 Polish Holstein-Friesian bulls genotyped by the Illumina BovineSNP50 Bead Chip. TagSNPs are selected for each of the subsets, as well as for the whole data set. The average reduction of the SNP number is 77.2% and is very similar in each sub-population. Differences in tagSNP selection between sub-populations are small. On average, 93.88% of the tagSNPs overlap between subsets. The study showed that differences in the genetic structure of the reference population have little influence on tagSNP selection.

Corresponding author
Hide All
Banos, G, Coffey, MP 2010. Short communication: characterization of the genome-wide linkage disequilibrium in 2 divergent selection lines of dairy cows. Journal of Dairy Science 93, 27752778.
Barendse, W, Reverter, A, Bunch, RJ, Harrison, BE, Barris, W, Thomas, MB 2007. A validated whole-genome association study of efficient food conversion in cattle. Genetics 176, 18931905.
Barrett, JC, Fry, B, Maller, J, Daly, MJ 2004. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263265.
Boehnke, M 2000. A look at linkage disequilibrium. Nature Genetics 25, 246247.
Calus, MPL 2010. Genomic breeding value prediction: methods and procedures. Animal 4, 157164.
Carlson, CS, Eberle, MA, Rieder, MJ, Quian, Y, Krygulak, L, Nickerson, DA 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. American Journal of Human Genetics 74, 106120.
de Bakker, PI, Yelensky, R, Pe'er, I, Gabriel, SB, Daly, MJ, Altshuler, D 2005. Efficiency and power in genetic association studies. Nature Genetics 37, 12171223.
de Roos, APW, Hayes, BJ, Spelman, RJ, Goddard, ME 2008. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics 179, 15031512.
Ding, K, Kullo, IJ 2007. Methods for the selection of tagging SNPs: a comparison of tagging efficiency and performance. European Journal of Human Genetics 15, 228236.
Gabriel, SB, Schaffner, SF, Nguyen, H, Moore, JM, Roy, J, Blumenstiel, B, Higgins, J, DeFelice, M, Lochner, A, Faggart, M, Liu-Cordero, SN, Rotimi, C, Adeyemo, A, Cooper, R, Ward, R, Lander, ES, Daly, MJ, Altshuler, D 2002. The structure of haplotype blocks in the human genome. Science 296, 22252229.
Gautier, M, Faraut, T, Moazami-Goudarzi, K, Navratil, V, Foglio, M, Grohs, C, Boland, A, Garnier, JG, Boichard, D, Lathrop, GM, Gut, IG, Eggen, A 2007. Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics 177, 10591070.
Ke, X, Miretti, MM, Broxholme, J, Hunt, S, Beck, S, Bentley, DR, Deloukas, P, Cardon, LR 2005. A comparison of tagging methods and their tagging space. Human Molecular Genetics 14, 27572767.
Khatkar, MS, Nicholas, FW, Collins, AR, Zenger, KR, Cavanagh, JAL, Barris, W, Schnabel, RD, Taylor, JF, Raadsma, HW 2008. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9, 187.
Khatkar, MS, Zenger, KR, Hobbs, M, Hawken, RJ, Cavanagh, JA, Barris, W, McClintock, AE, McClintock, S, Thomson, PC, Tier, B, Nicholas, FW, Raadsma, HW 2007. A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in Holstein-Friesian cattle. Genetics 176, 763772.
Kim, ES, Kirkpatrick, BW 2009. Linkage disequilibrium in the North American Holstein population. Animal Genetics 40, 279288.
LaFramboise, T 2009. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Research 37, 41814193.
Marques, E, Schnabel, RD, Stothard, P, Kolbehdari, D, Wang, Z, Taylor, JF, Moore, SS 2008. High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle. BMC Genetics 9, 45, doi:10.1186/1471-2156-9-45, Published online by BioMed Central Ltd.
Matukumalli, LK, Lawley, CT, Schnabel, RD, Taylor, JF, Allan, MF, Heaton, MP, O'Conell, J, Moore, SS, Smith, TP, Sonstegard, TS, Van Tassell, CP 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4(4), e5350, doi:10.1371/journal.pone.0005350, Published online by PLoS ONE.
McKay, SD, Schnabel, RD, Murdoch, BM, Matukumalli, LK, Aerts, J, Coppieters, W, Crews, D, Neto, ED, Gill, CA, Gao, C, Mannen, H, Stothard, P, Wang, Z, Van Tassell, CP, Williams, JL, Taylor, JF, Moore, SS 2007. Whole genome linkage disequilibrium maps in cattle. BMC Genetics 8, 74, doi:10.1186/1471-2156-8-74, Published online by BioMed Central Ltd.
Prasad, A, Schnabel, RD, McKay, SD, Murdoch, B, Stothard, P, Kolbehdari, D, Wang, Z, Taylor, JF, Moore, SS 2008. Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle. Animal Genetics 39, 597605.
Qanbari, S, Pimentel, EC, Tetens, J, Thaller, G, Lichtner, P, Sharifi, AR, Simianer, H 2010. The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics 41, 346356.
R Development Core Team 2010. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Sargolzaei, M, Schenkel, FS, Jansen, GB, Schaeffer, LR 2008. Extent of linkage disequilibrium in Holstein cattle in North America. Journal of Dairy Science 91, 21062117.
Schaeffer, LR 2006. Strategy for applying genome-wide selection in dairy cattle. Journal of Animal Breading and Genetics 123, 218223.
Villa-Angulo, R, Matukumalli, LK, Gill, CA, Choi, J, Van Tassell, CP, Grefenstette, JJ 2009. High-resolution haplo-type block structure in the cattle genome. BMC Genetics 10, 19, doi:10.1186/1471-2156-10-19, Published online by BioMed Central Ltd.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

  • ISSN: 1751-7311
  • EISSN: 1751-732X
  • URL: /core/journals/animal
Please enter your name
Please enter a valid email address
Who would you like to send this to? *


Type Description Title
Supplementary materials

Silesian Supplementary Material
Silesian S2

 PDF (662 KB)
662 KB
Supplementary materials

Silesian Supplementary Material
Silesian S1

 PDF (704 KB)
704 KB


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed