Cow genotyping strategies for genomic selection in a small dairy cattle population
Cow genotyping strategies for genomic selection in a small dairy cattle population
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DOI：
10.3168/jds.2016-11479
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发表时间：
2017-01-01
影响因子：
3.5
通讯作者：
Woolliams, J. A.
中科院分区：
文献类型：
--
作者：
Jenko, J.;Wiggans, G. R.;Woolliams, J. A.
本研究比较了不同的奶牛基因分型策略如何提高低数量奶牛品种的基因组估计育种值（EBV）的准确性。在这些品种中，很少有父系有后代记录，基因分型奶牛可以提高基因组EBV的准确性。根西岛品种是一种小型奶牛品种，全球约有14，000头记录个体。使用基因组EBV对来自英格兰和根西岛的根西岛奶牛的产奶量、脂肪产量、蛋白质产量和产犊间隔的表型进行预测，训练集包括197头基因分型公牛的去回归证明，其中奶牛使用不同的基因分型策略从1，440头基因分型奶牛中选出。预测的准确性进行了测试，使用10倍交叉验证之间的奶牛。使用4种不同的方法预测基因组EBV：（1）系谱BLUP，（2）仅使用公牛的基因组BLUP，（3）使用公牛和母牛的单变量基因组BLUP，以及（4）双变量基因组BLUP。与仅使用公牛相比，对具有表型的奶牛进行基因分型并使用其数据预测单核苷酸多态性效应增加了基因组EBV与表型之间的相关性，对于产奶量增加了0.163 +/- 0.022，对于脂肪产量增加了0.111 +/- 0.021，对于蛋白质产量增加了0.113 +/- 0.018;产犊间隔从低基数下降0.014 +/- 0.010是唯一的例外。公牛和母牛的表型间的遗传相关在所有产量性状上均约为0.6，与1之间存在显著差异。当使用双变量模型时，基因组EBV和表型之间的相关性仅发生非常小的变化。对所有奶牛进行基因分型总是更好的，但是当只有一半的奶牛进行基因分型时，与随机或定向选择方法相比，发散选择策略更好。30%的母牛在10倍中有8倍的产量性状保持上级。
This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds, few sires have progeny records, and genotyping cows can improve the accuracy of genomic EBV. The Guernsey breed is a small dairy cattle breed with approximately 14,000 recorded individuals worldwide. Predictions of phenotypes of milk yield, fat yield, protein yield, and calving interval were made for Guernsey cows from England and Guernsey Island using genomic EBV, with training sets including 197 de-regressed proofs of genotyped bulls, with cows selected from among 1,440 genotyped cows using different genotyping strategies. Accuracies of predictions were tested using 10-fold cross-validation among the cows. Genomic EBV were predicted using 4 different methods: (1) pedigree BLUP, (2) genomic BLUP using only bulls, (3) univariate genomic BLUP using bulls and cows, and (4) bivariate genomic BLUP. Genotyping cows with phenotypes and using their data for the prediction of single nucleotide polymorphism effects increased the correlation between genomic EBV and phenotypes compared with using only bulls by 0.163 +/- 0.022 for milk yield, 0.111 +/- 0.021 for fat yield, and 0.113 +/- 0.018 for protein yield; a decrease of 0.014 +/- 0.010 for calving interval from a low base was the only exception. Genetic correlation between phenotypes from bulls and cows were approximately 0.6 for all yield traits and significantly different from 1. Only a very small change occurred in correlation between genomic EBV and phenotypes when using the bivariate model. It was always better to genotype all the cows, but when only half of the cows were genotyped, a divergent selection strategy was better compared with the random or directional selection approach. Divergent selection of 30% of the cows remained superior for the yield traits in 8 of 10 folds.