Sequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle.
Sequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle.
复制标题
DOI：
10.1186/s12711-016-0259-0
复制
发表时间：
2016-11-04
期刊：
影响因子：
--
通讯作者：
Lund MS
中科院分区：
文献类型：
--
作者：
van den Berg I;Boichard D;Lund MS
序列数据可以潜在地提高基因组预测的可靠性，因为这些数据包括致病突变，而不是依赖于致病突变和预测变体之间的连锁不平衡（LD）。然而，致病突变的位置尚不清楚，并且许多与致病突变一起处于低LD的变异的存在可能会降低预测的可靠性。我们的目的是研究在多品种全基因组关联研究（GWAS）中发现的牛奶、脂肪和蛋白质产量的数量性状位点（QTL）变异的使用是否会提高荷斯坦牛、泽西牛和丹麦红牛单品种和多品种基因组预测的可靠性。本研究比较了品种内和多品种预测中测试不同预测标记选择策略的各种场景。对于所有品种和性状，与使用50 K SNP阵列进行品种内预测相比，使用从多品种GWAS中选择的变异可显著提高预测可靠性。可靠性高度依赖于预测标记的选择，导致最高可靠性的情景因品种和性状而异。虽然全基因组序列变异在品种间的基因组相关性较低，但产生最高可靠性的QTL变异的影响在品种间高度相关。我们的研究结果表明，使用序列变异（位于多品种GWAS中检测到的QTL峰值附近）可以提高基因组预测的可靠性。本文的在线版本（doi:10.1186/s12711-016-0259-0）包含补充材料，可供授权用户使用。
Sequence data can potentially increase the reliability of genomic predictions, because such data include causative mutations instead of relying on linkage disequilibrium (LD) between causative mutations and prediction variants. However, the location of the causative mutations is not known, and the presence of many variants that are in low LD with the causative mutations may reduce prediction reliability. Our objective was to investigate whether the use of variants at quantitative trait loci (QTL) that are identified in a multi-breed genome-wide association study (GWAS) for milk, fat and protein yield would increase the reliability of within- and multi-breed genomic predictions in Holstein, Jersey and Danish Red cattle. A wide range of scenarios that test different strategies to select prediction markers, for both within-breed and multi-breed prediction, were compared. For all breeds and traits, the use of variants selected from a multi-breed GWAS resulted in substantial increases in prediction reliabilities compared to within-breed prediction using a 50 K SNP array. Reliabilities depended highly on the choice of the prediction markers, and the scenario that led to the highest reliability varied between breeds and traits. While genomic correlations across breeds were low for genome-wide sequence variants, the effects of the QTL variants that yielded the highest reliabilities were highly correlated across breeds. Our results show that the use of sequence variants, which are located near peaks of QTL that are detected in a multi-breed GWAS, can increase reliability of genomic predictions. The online version of this article (doi:10.1186/s12711-016-0259-0) contains supplementary material, which is available to authorized users.
登录
查看更多内容
DOI：
10.1186/1297-9686-42-5
发表时间：
2010-02-19
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Habier D;Tetens J;Seefried FR;Lichtner P;Thaller G
通讯作者：
Thaller G
DOI：
10.1186/1297-9686-43-19
发表时间：
2011-05-17
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Liu Z;Seefried FR;Reinhardt F;Rensing S;Thaller G;Reents R
通讯作者：
Reents R
影响因子：
3.5
作者：
Brondum, R. F.;Su, G.;Lund, M. S.
通讯作者：
Lund, M. S.
影响因子：
2.9
作者：
Kapell, Dagmar N. R. G.;Sorensen, Daniel;Roehe, Rainer
通讯作者：
Roehe, Rainer
影响因子：
4.4
作者：
Cole JB;Wiggans GR;Ma L;Sonstegard TS;Lawlor TJ Jr;Crooker BA;Van Tassell CP;Yang J;Wang S;Matukumalli LK;Da Y
通讯作者：
Da Y