Department of Animal Science, Michigan State University, East Lansing, MI, USA.
BMC Genomics. 2012 Jan 17;13:24. doi: 10.1186/1471-2164-13-24.
The success of marker assisted selection depends on the amount of linkage disequilibrium (LD) across the genome. To implement marker assisted selection in the swine breeding industry, information about extent and degree of LD is essential. The objective of this study is to estimate LD in four US breeds of pigs (Duroc, Hampshire, Landrace, and Yorkshire) and subsequently calculate persistence of phase among them using a 60 k SNP panel. In addition, we report LD when using only a fraction of the available markers, to estimate persistence of LD over distance.
Average r2 between adjacent SNP across all chromosomes was 0.36 for Landrace, 0.39 for Yorkshire, 0.44 for Hampshire and 0.46 for Duroc. For markers 1 Mb apart, r2 ranged from 0.15 for Landrace to 0.20 for Hampshire. Reducing the marker panel to 10% of its original density, average r2 ranged between 0.20 for Landrace to 0.25 for Duroc. We also estimated persistence of phase as a measure of prediction reliability of markers in one breed by those in another and found that markers less than 10 kb apart could be predicted with a maximal accuracy of 0.92 for Landrace with Yorkshire.
Our estimates of LD, although in good agreement with previous reports, are more comprehensive and based on a larger panel of markers. Our estimates also confirmed earlier findings reporting higher LD in pigs than in American Holstein cattle, especially at increasing marker distances (> 1 Mb). High average LD (r2 > 0.4) between adjacent SNP found in this study is an important precursor for the implementation of marker assisted selection within a livestock species.Results of this study are relevant to the US purebred pig industry and critical for the design of programs of whole genome marker assisted evaluation and selection. In addition, results indicate that a more cost efficient implementation of marker assisted selection using low density panels with genotype imputation, would be feasible for these breeds.
标记辅助选择的成功取决于基因组中连锁不平衡（LD）的程度。为了在养猪业中实施标记辅助选择，了解 LD 的程度和范围至关重要。本研究的目的是估计四个美国猪品种（杜洛克、汉普夏、长白和约克夏）的 LD，并使用 60kSNP 面板计算它们之间的相位持续时间。此外，我们还报告了仅使用部分可用标记时的 LD，以估计 LD 随距离的持续时间。
所有染色体上相邻 SNP 之间的平均 r2 为 Landrace 为 0.36，Yorkshire 为 0.39，Hampshire 为 0.44，Duroc 为 0.46。对于相隔 1Mb 的标记，r2 范围从 Landrace 的 0.15 到 Hampshire 的 0.20。将标记面板减少到原始密度的 10%，平均 r2 范围从 Landrace 的 0.20 到 Duroc 的 0.25。我们还估计了相位持续时间，作为一种衡量一个品种的标记在另一个品种中的预测可靠性的指标，发现相隔不到 10kb 的标记可以用最大的准确性预测，Landrace 与 Yorkshire 的准确率为 0.92。
我们的 LD 估计值虽然与以前的报告基本一致，但更全面，并且基于更大的标记面板。我们的估计还证实了早期的发现，即在猪中 LD 高于美国荷斯坦奶牛，特别是在增加标记距离（>1Mb）时。本研究中发现的相邻 SNP 之间的平均 LD（r2>0.4）较高，是在一个家畜物种中实施标记辅助选择的重要前提。本研究的结果与美国纯种猪产业相关，对全基因组标记辅助评估和选择计划的设计至关重要。此外，结果表明，使用基因型推断的低密度面板更经济高效地实施标记辅助选择对于这些品种是可行的。
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