title: Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip.
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.
authors.affiliation: CSIRO Agriculture Flagship, St Lucia, Qld 4067, Australia.
authors.forename: James W
authors.initials: JW
authors.lastname: Kijas
authors.forename: Laercio
authors.initials: L
authors.lastname: Porto-Neto
authors.forename: Sonja
authors.initials: S
authors.lastname: Dominik
authors.forename: Antonio
authors.initials: A
authors.lastname: Reverter
authors.forename: Rowan
authors.initials: R
authors.lastname: Bunch
authors.forename: Russell
authors.initials: R
authors.lastname: McCulloch
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Hayes
authors.forename: Rudiger
authors.initials: R
authors.lastname: Brauning
authors.forename: John
authors.initials: J
authors.lastname: McEwan
mesh_terms: D000818:Animals; D014644:Genetic Variation; D005828:Genetics, Population; D015810:Linkage Disequilibrium; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D034561:Sheep, Domestic / Q000235:genetics*
keywords: breeds; genetic diversity; genomics