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Permanent link (DOI): https://doi.org/10.7939/R3Q52FH2X

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High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle Open Access

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Author or creator
Marques, E.
Schnabel, R.
Stothard, P.
Kolbehdari, D.
Wang, Z.
Taylor, J. F.
Moore, S. S.
Additional contributors
Subject/Keyword
chromosomes
cattle/genetics
mammalian/genetics
mapping/methods
linkage disequilibrium
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
Background Linkage disequilibrium (LD) maps can provide a wealth of information on specific marker-phenotype relationships, especially in areas of the genome where positional candidate genes with similar functions are located. A recently published high resolution radiation hybrid map of bovine chromosome 14 (BTA14) together with the bovine physical map have enabled the creation of more accurate LD maps for BTA14 in both dairy and beef cattle. Results Over 500 Single Nucleotide Polymorphism (SNP) markers from both Angus and Holstein animals had their phased haplotypes estimated using GENOPROB and their pairwise r2 values compared. For both breeds, results showed that average LD extends at moderate levels up to 100 kilo base pairs (kbp) and falls to background levels after 500 kbp. Haplotype block structure analysis using HAPLOVIEW under the four gamete rule identified 122 haplotype blocks for both Angus and Holstein. In addition, SNP tagging analysis identified 410 SNPs and 420 SNPs in Holstein and Angus, respectively, for future whole genome association studies on BTA14. Correlation analysis for marker pairs common to these two breeds confirmed that there are no substantial correlations between r-values at distances over 10 kbp. Comparison of extended haplotype homozygosity (EHH), which calculates the LD decay away from a core haplotype, shows that in Holstein there is long range LD decay away from the DGAT1 region consistent with the selection for milk fat % in this population. Comparison of EHH values for Angus in the same region shows very little long range LD. Conclusion Overall, the results presented here can be applied in future single or haplotype association analysis for both populations, aiding in confirming or excluding potential polymorphisms as causative mutations, especially around Quantitative Trait Loci regions. In addition, knowledge of specific LD information among markers will aid the research community in selecting appropriate markers for whole genome association studies.
Date created
2008
DOI
doi:10.7939/R3Q52FH2X
License information
Attribution 4.0 International
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Citation for previous publication
Marques, E., R. Schnabel,Stothard, P., D. Kolbehdari, Wang, Z., J. F. Taylor, and S. S. Moore. (2008). High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle. BMC Genetics, 9(45), 12 pg.  http://dx.doi.org/10.1186/1471-2156-9-45

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File title: Abstract
File title: 1471-2156-9-45.fm
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