Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip
Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip
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DOI：
10.1111/age.12197
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发表时间：
2014-10-01
期刊：
影响因子：
2.4
通讯作者：
McEwan, John
中科院分区：
文献类型：
--
作者：
Kijas, James W.;Porto-Neto, Laercio;McEwan, John
遗传位点之间的连锁不平衡（LD）的程度对关联研究和基因组预测的准确性都有影响。为了验证LD在不同绵羊品种中的持续性，使用了两个SNP基因分型平台。首先，使用绵羊SNP50 BeadChip（49034个位点）获得的63个品种的现有SNP基因型被用来估计LD衰减的遗传多样性水平的对比人群。鉴于缺乏标记对分离的SNP50珠芯片上的短的物理距离，基因分型随后进行了四个品种，使用最近开发的绵羊HD珠芯片，测定约600000单核苷酸多态性，平均基因组间距为5 kb。这有助于在短基因组距离上高度准确地估计LD（
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 (49034 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 600000 SNPs with an average genomic spacing of 5 kb. This facilitated a highly accurate estimate of LD over short genomic distances (