Linkage disequilibrium (LD) was measured by r2 for a sample of chromosome from the New Zealand Jersey population. Three hundred and thirty-nine single nucleotide polymorphic (SNP) markers from the Affymetrix GeneChip BovineMapping 10 K SNP Kit were located on chromosome. Forty maternal Jersey chromosomes were inferred from sire and progeny genotypes. Average pairwise LD was approximately 0.1 for markers within 1 Mb of each other and dropped to 0.04 for markers within 5 Mb. The level of redundancy in the dataset, measured by identifying how many markers had another marker with a r2 value >0.9, was 35%. The majority of the markers did not have another marker in strong LD. We concluded that from this dataset that there would be a need to have more SNPs than that present on the Affymetrix 10 K panel, for fine mapping to the causative mutation and for Genomic Selection.

Richard Spelman, W. Coppieters

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 22.21, 2006
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