Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

de Roos, A. P. W., Hayes, B. J., Spelman, R. J. and Goddard, M. E. (2008) Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics, 179 3: 1503-1512. doi:10.1534/genetics.107.084301


Author de Roos, A. P. W.
Hayes, B. J.
Spelman, R. J.
Goddard, M. E.
Title Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle
Journal name Genetics   Check publisher's open access policy
ISSN 0016-6731
1943-2631
Publication date 2008-07-01
Sub-type Article (original research)
DOI 10.1534/genetics.107.084301
Volume 179
Issue 3
Start page 1503
End page 1512
Total pages 10
Place of publication Bethesda, MD, United States
Publisher Genetics Society of America
Language eng
Formatted abstract
When a genetic marker and a quantitative trait locus (QTL) are in linkage disequilibrium (LD) in one population, they may not be in LD in another population or their LD phase may be reversed. The objectives of this study were to compare the extent of LD and the persistence of LD phase across multiple cattle populations. LD measures r and r2 were calculated for syntenic marker pairs using genomewide single-nucleotide polymorphisms (SNP) that were genotyped in Dutch and Australian Holstein-Friesian (HF) bulls, Australian Angus cattle, and New Zealand Friesian and Jersey cows. Average r2 was ∼0.35, 0.25, 0.22, 0.14, and 0.06 at marker distances 10, 20, 40, 100, and 1000 kb, respectively, which indicates that genomic selection within cattle breeds with r2 ≥ 0.20 between adjacent markers would require ∼50,000 SNPs. The correlation of r values between populations for the same marker pairs was close to 1 for pairs of very close markers (<10 kb) and decreased with increasing marker distance and the extent of divergence between the populations. To find markers that are in LD with QTL across diverged breeds, such as HF, Jersey, and Angus, would require ∼300,000 markers.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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