Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350, USA.
J Dairy Sci. 2011 Nov;94(11):5673-82. doi: 10.3168/jds.2011-4500.
Genomic measures of relationship and inbreeding within and across breeds were compared with pedigree measures using genotypes for 43,385 loci of 25,219 Holsteins, 3,068 Jerseys, and 872 Brown Swiss. Adjustment factors allow genomic and pedigree relationships to match more closely within breeds and in multibreed populations and were estimated using means and regressions of genomic on pedigree relationships and allele frequencies in base populations. Correlations of genomic relationships with pedigree inbreeding were higher within each breed when an allele frequency of 0.5, rather than base population frequencies, was used, whereas correlations of average genomic relationships with average pedigree relationships and also reliabilities of genomic evaluations were higher using base population frequencies. Allele frequencies differed in the 3 breeds and were correlated by 0.65 to 0.67 when estimated from genotyped animals compared with 0.72 to 0.74 when estimated from breed base populations. The largest difference in allele frequency was between Holstein and the other breeds on chromosome Bos taurus autosome 4 near a gene affecting appearance of white skin patches (vitiligo) in humans. Each animal's breed composition was predicted very accurately with a standard deviation of <3% using regressions on genotypes at all loci or less accurately with a standard deviation of <6% using subsets of loci. Genomic future inbreeding (half an animal's mean genomic relationship to current animals of the same breed) was correlated by 0.75 to 0.94 with expected future inbreeding (half the average pedigree relationship). Correlations of both were slightly higher with parent averages than with genomic evaluations for net merit of young Holstein bulls. Thus, rates of increase in genomic and pedigree inbreeding per generation should be slightly reduced with genomic selection, in agreement with previous simulations. Genomic inbreeding and future inbreeding have been provided with individual genomic predictions since 2008. New methods to adjust pedigree and genomic relationship matrices so that they match may provide an improved basis for multibreed genomic evaluation. Positive definite matrices can be obtained by adjusting pedigree relationships for covariances among base animals within breed, whereas adjusting genomic relationships to match pedigree relationships can introduce negative eigenvalues. Pedigree relationship matrices ignore common ancestry shared by base animals within breed and may not approximate genomic relationships well in multibreed populations.
比较了 25219 头荷斯坦奶牛、3068 头泽西牛和 872 头瑞士褐牛的 43385 个基因座的基因型的基因组亲缘关系和近交系数与系谱亲缘关系的度量，使用了调整因子可以在品种内和多品种群体中更紧密地匹配基因组和系谱关系，并使用基于群体的基因组对系谱关系和等位基因频率的均值和回归来估计。当使用等位基因频率为 0.5 而不是基础群体频率时，每个品种内的基因组关系与系谱近交的相关性更高，而使用基础群体频率时，平均基因组关系与平均系谱关系的相关性以及基因组评估的可靠性更高。在 3 个品种中，等位基因频率不同，与通过基因分型动物估计的相比，与从品种基础群体估计的相比，差异在 0.65 到 0.67 之间，而与 0.72 到 0.74 之间。在人类影响白色皮肤斑块（白癜风）出现的基因附近的牛科染色体 Bos taurus 常染色体 4 上，荷斯坦牛和其他品种之间的等位基因频率差异最大。使用所有基因座上的基因型回归或使用基因座子集以标准差 <6%更不准确地预测每个动物的品种组成，标准差 <3%。基因组未来近交（同一品种当前动物的一半动物平均基因组关系）与预期未来近交（平均系谱关系的一半）的相关性为 0.75 到 0.94。对于年轻荷斯坦公牛的净遗传优势，父母平均值的相关性略高于基因组评估。因此，与之前的模拟结果一致，随着基因组选择的使用，每代的基因组和系谱近交率应略有降低。自 2008 年以来，已经为个体基因组预测提供了基因组近交和未来近交。调整系谱和基因组关系矩阵以匹配的新方法可能为多品种基因组评估提供更好的基础。通过调整品种内基础动物之间的协方差，可以获得正定的系谱关系矩阵，而调整基因组关系以匹配系谱关系可能会引入负特征值。系谱关系矩阵忽略了品种内基础动物之间的共同祖先，并且在多品种群体中可能无法很好地近似基因组关系。
