Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population.
Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population.
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DOI：
10.1186/1471-2164-15-1171
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发表时间：
2014-12-23
期刊：
影响因子：
4.4
通讯作者：
Lund MS
中科院分区：
文献类型：
--
作者：
Cuyabano BC;Su G;Lund MS
一个单倍型的方法，利用高密度的数据在奶牛的基因组预测作为一种替代单标记的方法。假设单倍型与数量性状基因座（QTL）的连锁不平衡（LD）比单个标记更强，本研究的重点是使用单倍型块（单倍块）作为基因组预测的解释变量。基于标记物之间的LD构建单倍区组，这允许变量减少。然后，单倍体被用来预测三个经济上重要的性状（乳蛋白，生育力和乳腺炎）在北欧荷斯坦人口。与常用的个体单核苷酸多态性（SNP）方法相比，单块方法提高了预测准确性。此外，使用平均LD阈值来定义单倍块（任何两个标记之间的LD≥0.45）增加了所有三个性状的预测准确度，尽管对于乳蛋白的改善最显著（与单个SNP方法相比，预测准确度提高高达3.1%）。进行了Hotelling t检验，证实了乳蛋白预测准确性的提高。因为表型值是以去回归证明的形式，所以乳蛋白的准确性提高可能是由于与乳腺炎和生育力数据的可靠性相比，该性状的数据可靠性更高。最佳线性无偏预测（BLUP）和贝叶斯混合模型之间的比较也表明，贝叶斯模型在每种情况下的牛奶蛋白质性状，并在某些情况下生育率产生最准确的预测。基因组单块预测方法是一种很有前途的动物育种基因组选择方法。基于LD构建单块减少了变量的数量，而不会丢失信息。该方法在未来的基因组预测中可能发挥重要作用。
A haplotype approach to genomic prediction using high density data in dairy cattle as an alternative to single-marker methods is presented. With the assumption that haplotypes are in stronger linkage disequilibrium (LD) with quantitative trait loci (QTL) than single markers, this study focuses on the use of haplotype blocks (haploblocks) as explanatory variables for genomic prediction. Haploblocks were built based on the LD between markers, which allowed variable reduction. The haploblocks were then used to predict three economically important traits (milk protein, fertility and mastitis) in the Nordic Holstein population. The haploblock approach improved prediction accuracy compared with the commonly used individual single nucleotide polymorphism (SNP) approach. Furthermore, using an average LD threshold to define the haploblocks (LD≥0.45 between any two markers) increased the prediction accuracies for all three traits, although the improvement was most significant for milk protein (up to 3.1 % improvement in prediction accuracy, compared with the individual SNP approach). Hotelling’s t-tests were performed, confirming the improvement in prediction accuracy for milk protein. Because the phenotypic values were in the form of de-regressed proofs, the improved accuracy for milk protein may be due to higher reliability of the data for this trait compared with the reliability of the mastitis and fertility data. Comparisons between best linear unbiased prediction (BLUP) and Bayesian mixture models also indicated that the Bayesian model produced the most accurate predictions in every scenario for the milk protein trait, and in some scenarios for fertility. The haploblock approach to genomic prediction is a promising method for genomic selection in animal breeding. Building haploblocks based on LD reduced the number of variables without the loss of information. This method may play an important role in the future genomic prediction involving while genome sequences.
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影响因子：
4.1
作者：
Meuwissen, Theo H. E.
通讯作者：
Meuwissen, Theo H. E.
影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
影响因子：
1.9
作者：
North, B. V.;Sham, P. C.;Curtis, D.
通讯作者：
Curtis, D.
影响因子：
1.8
作者：
Chapman, JM;Cooper, JD;Clayton, DG
通讯作者：
Clayton, DG
DOI：
10.1016/s0301-6226(00)00255-4
发表时间：
2001-05-01
期刊：
LIVESTOCK PRODUCTION SCIENCE
影响因子：
--
作者：
Schaeffer, LR
通讯作者：
Schaeffer, LR