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

Kijas, James W., Porto-Neto, Laercio, Dominik, Sonja, Reverter, Antonio, Bunch, Rowan, McCulloch, Russell, Hayes, Ben J., Brauning, Rudiger and McEwan, John (2014) Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip. Animal Genetics, 45 5: 754-757. doi:10.1111/age.12197


Author Kijas, James W.
Porto-Neto, Laercio
Dominik, Sonja
Reverter, Antonio
Bunch, Rowan
McCulloch, Russell
Hayes, Ben J.
Brauning, Rudiger
McEwan, John
Title Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip
Journal name Animal Genetics   Check publisher's open access policy
ISSN 1365-2052
0268-9146
Publication date 2014-10
Sub-type Article (original research)
DOI 10.1111/age.12197
Open Access Status Not yet assessed
Volume 45
Issue 5
Start page 754
End page 757
Total pages 4
Place of publication Chichester, West Sussex United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
Abstract 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 (<30 kb) and revealed LD varies considerably between sheep breeds. Further, sheep appear to contain generally lower levels of LD than do other domestic species, likely a reflection of aspects of their past population history.
Keyword Breeds
Genetic diversity
Genomics
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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