The effect of genomic information on optimal contribution selection in livestock breeding programs.
The effect of genomic information on optimal contribution selection in livestock breeding programs.
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DOI：
10.1186/1297-9686-45-44
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发表时间：
2013-10-30
期刊：
影响因子：
--
通讯作者：
van der Werf JH
中科院分区：
文献类型：
--
作者：
Clark SA;Kinghorn BP;Hickey JM;van der Werf JH
动物育种计划的长期利益要求增加遗传价值与保持多样性（由于近亲繁殖而丧失）的需要相平衡。这可以通过使用最优贡献选择来实现。高密度DNA标记信息的可用性使得将基因组数据整合到最优贡献选择中成为可能，但这也提出了一个问题，即这些信息如何影响遗传优点和多样性之间的平衡。基于模拟数据和真实数据，研究了基因组信息在奶牛最优贡献选择中的作用。当使用基于亲本平均值、基因组或后代测试信息的估计育种值时，我们比较了在不同水平的共同祖先限制下选定动物的遗传优点。此外，我们估计了由于家族内差异而导致的估计育种值变化的比例。基因组育种估计值的优化选择提高了遗传增益。在近交限制政策下，使用基因组而不是基于系谱的共同祖先测量进一步增加了遗传优点。使用基因组关系而不是系谱关系来限制近亲繁殖只有在种群由许多大的全同胞家庭组成时才有显著效果；在同父异母的家庭结构中，没有观察到差异。在奶牛的真实数据中，基于基因组估计育种值的最佳贡献选择允许在低至中等近交水平下进一步改进遗传优点。基因组育种估计值比亲本平均育种值更准确，且显示出更多的家族内变异；对于基因组估计的育种值，30%至40%的变异是由于家族内的差异。最后，在实际数据中，通过系谱或基因组关系来限制近亲繁殖没有区别。在最优贡献选择中，基因组估计育种值的使用增加了遗传增益。基因组估计育种值更准确，显示出更多的家族内变异，这导致相同的近亲繁殖限制的遗传收益更高。使用基因组关系来限制近亲繁殖并没有提供额外的收益，除非是在非常大的全同胞家庭中。
Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity. The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences. Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data. The use of genomic estimated breeding values increased genetic gain in optimal contribution selection. Genomic estimated breeding values were more accurate and showed more within-family variation, which led to higher genetic gains for the same restriction on inbreeding. Using genomic relationships to restrict inbreeding provided no additional gain, except in the case of very large full-sib families.
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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
影响因子：
3.3
作者：
Habier, D.;Fernando, R. L.;Dekkers, J. C. M.
通讯作者：
Dekkers, J. C. M.
DOI：
10.1186/1297-9686-44-4
发表时间：
2012-02-09
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Clark SA;Hickey JM;Daetwyler HD;van der Werf JH
通讯作者：
van der Werf JH
影响因子：
1.5
作者：
Hayes, B. J.;Visscher, P. M.;Goddard, M. E.
通讯作者：
Goddard, M. E.
影响因子：
1.5
作者：
Hill, W. G.;Weir, B. S.
通讯作者：
Weir, B. S.