Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Apr 24:10:18.
doi: 10.1186/1471-2156-10-18.

A high density linkage map of the bovine genome

Juan A Arias  1 , Mike Keehan, Paul Fisher, Wouter Coppieters, Richard Spelman
Affiliations

A high density linkage map of the bovine genome

Juan A Arias et al. BMC Genet. .

Abstract

Background: Recent technological advances have made it possible to efficiently genotype large numbers of single nucleotide polymorphisms (SNPs) in livestock species, allowing the production of high-density linkage maps. Such maps can be used for quality control of other SNPs and for fine mapping of quantitative trait loci (QTL) via linkage disequilibrium (LD).

Results: A high-density bovine linkage map was constructed using three types of markers. The genotypic information was obtained from 294 microsatellites, three milk protein haplotypes and 6769 SNPs. The map was constructed by combining genetic (linkage) and physical information in an iterative mapping process. Markers were mapped to 3,155 unique positions; the 6,924 autosomal markers were mapped to 3,078 unique positions and the 123 non-pseudoautosomal and 19 pseudoautosomal sex chromosome markers were mapped to 62 and 15 unique positions, respectively. The linkage map had a total length of 3,249 cM. For the autosomes the average genetic distance between adjacent markers was 0.449 cM, the genetic distance between unique map positions was 1.01 cM and the average genetic distance (cM) per Mb was 1.25.

Conclusion: There is a high concordance between the order of the SNPs in our linkage map and their physical positions on the most recent bovine genome sequence assembly (Btau 4.0). The linkage maps provide support for fine mapping projects and LD studies in bovine populations. Additionally, the linkage map may help to resolve positions of unassigned portions of the bovine genome.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Marker locations on bovine genome sequence autosomes. Linkage maps for bovine autosomal chromosomes are presented here. Vertical lines symbolize bovine chromosomes. Horizontal lines on vertical lines represent locations of markers in chromosomes. Length of horizontal lines is proportional to number of markers at same location.
Figure 2
Figure 2
Comparison of marker linkage map order with positions in the bovine genome sequence assembly (Btau 4.0) [32].
Figure 3
Figure 3
Mapping flow chart. (1) Construction of low-density linkage map. (2) Construction of ARTIFICIAL LINKAGE MAP (ALMI). (3) and (4) Additional SNPs mapping loops. (5) SNP insertion phase. LDM: Low-density microsatellite based linkake map. LD1: Low-density microsatellite linkage map. LD2: Low-density SNP linkage map. LD3: Low-density microsatellite-SNP linkage map. LOD: Log of Odds.
See this image and copyright information in PMC

References

    1. Dearlove AM. High throughput genotyping technologies. Brief Funct Genomic Proteomic. 2002;1:139–150. doi: 10.1093/bfgp/1.2.139. - DOI - PubMed
    1. Syvänen AC. Toward genome-wide SNP genotyping. Nat Genet. 2005;37:s5–s10. doi: 10.1038/ng1558. - DOI - PubMed
    1. McKay SD, Schnabel SD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Dias Neto E, Gill CA, Gao C, Mannen H, Stothard P, Wang Z, Van Tassel CP, Williams JL, Taylor JF, Moore SS. Whole genome linkage disequilibrium maps in cattle. BMC Genetics. 2007;8:74. doi: 10.1186/1471-2156-8-74. - DOI - PMC - PubMed
    1. Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JAL, Barris W, McClintock AE, McClintock S, Thomson PC, Tier B, Nicholas FW, Raadsma HW. A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in Holstein-Friesian cattle. Genetics. 2007;176:763–772. doi: 10.1534/genetics.106.069369. - DOI - PMC - PubMed
    1. Orr N, Bekker V, Chanock S. Genetic association studies: marking them well. J Infect Dis. 2006;194:1475–1477. doi: 10.1086/508552. - DOI - PubMed