Linkage disequilibrium over short physical distances measured in sheep using a high‐density SNP chip

The extent of linkage disequilibrium (LD) between genetic loci has implications for both association studies and the accuracy of genomic prediction. To characterise the persistence of LD in diverse sheep breeds, two SNP genotyping platforms were used. First, existing SNP genotypes from 63 breeds obt...

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Bibliographic Details
Published in:Animal genetics 2014-10, Vol.45 (5), p.754-757
Main Authors: Kijas, James W, Porto‐Neto, Laercio, Dominik, Sonja, Reverter, Antonio, Bunch, Rowan, McCulloch, Russell, Hayes, Ben J, Brauning, Rudiger, McEwan, John
Format: Article
Language:English
Subjects:
Animals
breeds
genetic diversity
Genetic Variation
Genetics, Population
genomics
genotype
genotyping
Linkage Disequilibrium
loci
Oligonucleotide Array Sequence Analysis
Polymorphism, Single Nucleotide
prediction
sheep
sheep breeds
Sheep, Domestic - genetics
single nucleotide polymorphism
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Summary:The extent of linkage disequilibrium (LD) between genetic loci has implications for both association studies and the accuracy of genomic prediction. To characterise the persistence of LD in diverse sheep breeds, two SNP genotyping platforms were used. First, existing SNP genotypes from 63 breeds obtained using the ovine SNP50 BeadChip (49 034 loci) were used to estimate LD decay in populations with contrasting levels of genetic diversity. Given the paucity of marker pairs separated by short physical distances on the SNP50 BeadChip, genotyping was subsequently performed for four breeds using the recently developed ovine HD BeadChip that assays approximately 600 000 SNPs with an average genomic spacing of 5 kb. This facilitated a highly accurate estimate of LD over short genomic distances (
ISSN:0268-9146
1365-2052
DOI:10.1111/age.12197