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.

journal_name

Anim Genet

journal_title

Animal genetics

authors

Kijas JW,Porto-Neto L,Dominik S,Reverter A,Bunch R,McCulloch R,Hayes BJ,Brauning R,McEwan J,International Sheep Genomics Consortium.

doi

10.1111/age.12197

subject

Has Abstract

pub_date

2014-10-01 00:00:00

pages

754-7

issue

5

eissn

0268-9146

issn

1365-2052

journal_volume

45

pub_type

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