Estimation of additive and non-additive genetic effects for fertility and reproduction traits in North American Holstein cattle using genomic information
Estimation of additive and non-additive genetic effects for fertility and reproduction traits in North American Holstein cattle using genomic information
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DOI：
10.1111/jbg.12466
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发表时间：
2020-01-07
影响因子：
2.6
通讯作者：
Schenkel, Flavio S.
中科院分区：
文献类型：
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作者：
Alves, Kristen;Brito, Luiz F.;Schenkel, Flavio S.
在动物育种程序中，由于数据结构(如谱系不完整)、计算限制和模型的过度参数化，非加性遗传效应通常被忽略。然而，非加性遗传效应可能在家畜繁殖力和繁殖力等复杂性状的表达中发挥重要作用。本研究利用系谱和基因组关系矩阵，对荷斯坦牛各种繁殖力和繁殖性状的加性和非加性遗传效应的遗传方差分量进行了估计。使用了四个线性模型：(A)加性遗传模型；(B)既有加性效应又有上位性(加性)遗传效应的模型；(C)既有加性效应又有显性效应的模型；以及(D)包括加性、上位性和显性遗传效应的完整模型。分析了9个肥力和繁殖性状，并分别对小母牛(N=5,825)和母牛(N=6,090)运行模型。对于某些性状，非加性遗传效应对表型变异的解释比例大于加性效应，说明上位性、显性或它们的组合具有重要意义。上位性遗传效应对总表型变异的贡献率大于显性遗传效应。虽然这些模型在遗传方差分量的分配上有很大差异，但包含非加性遗传效应的模型并不比基于Akaike信息标准的加性模型显示出明显的优势。方差分量的划分导致完全基于奶牛在模型之间的加性遗传效应对奶牛进行重新排序，这表明调整非加性遗传效应可能会影响奶牛育种计划中的选择决策。这些结果表明，非加性遗传效应在荷斯坦牛的某些繁殖力和繁殖性状中起重要作用。
Non-additive genetic effects are usually ignored in animal breeding programs due to data structure (e.g., incomplete pedigree), computational limitations and over-parameterization of the models. However, non-additive genetic effects may play an important role in the expression of complex traits in livestock species, such as fertility and reproduction traits. In this study, components of genetic variance for additive and non-additive genetic effects were estimated for a variety of fertility and reproduction traits in Holstein cattle using pedigree and genomic relationship matrices. Four linear models were used: (a) an additive genetic model; (b) a model including both additive and epistatic (additive by additive) genetic effects; (c) a model including both additive and dominance effects; and (d) a full model including additive, epistatic and dominance genetic effects. Nine fertility and reproduction traits were analysed, and models were run separately for heifers (N = 5,825) and cows (N = 6,090). For some traits, a larger proportion of phenotypic variance was explained by non-additive genetic effects compared with additive effects, indicating that epistasis, dominance or a combination thereof is of great importance. Epistatic genetic effects contributed more to the total phenotypic variance than dominance genetic effects. Although these models varied considerably in the partitioning of the components of genetic variance, the models including a non-additive genetic effect did not show a clear advantage over the additive model based on the Akaike information criterion. The partitioning of variance components resulted in a re-ranking of cows based solely on the cows' additive genetic effects between models, indicating that adjusting for non-additive genetic effects could affect selection decisions made in dairy cattle breeding programs. These results suggest that non-additive genetic effects play an important role in some fertility and reproduction traits in Holstein cattle.