Animal Science Unit, Gembloux Agricultural University, B-5030 Gembloux, Belgium.
Animal. 2007 Feb;1(1):21-8. doi: 10.1017/S1751731107392628.
Gene content is the number of copies of a particular allele in a genotype of an animal. Gene content can be used to study additive gene action of candidate gene. Usually genotype data are available only for a part of population and for the rest gene contents have to be calculated based on typed relatives. Methods to calculate expected gene content for animals on large complex pedigrees are relatively complex. In this paper we proposed a practical method to calculate gene content using a linear regression. The method does not estimate genotype probabilities but these can be approximated from gene content assuming Hardy-Weinberg proportions. The approach was compared with other methods on multiple simulated data sets for real bovine pedigrees of 1 082 and 907 903 animals. Different allelic frequencies (0.4 and 0.2) and proportions of the missing genotypes (90, 70, and 50%) were considered in simulation. The simulation showed that the proposed method has similar capability to predict gene content as the iterative peeling method, however it requires less time and can be more practical for large pedigrees. The method was also applied to real data on the bovine myostatin locus on a large dual-purpose Belgian Blue pedigree of 235 133 animals. It was demonstrated that the proposed method can be easily adapted for particular pedigrees.
基因含量是动物基因型中特定等位基因的拷贝数。基因含量可用于研究候选基因的累加基因作用。通常，基因型数据仅可用于部分群体，而对于其余部分，必须基于已分型的亲属来计算基因含量。对于具有大型复杂系谱的动物，计算预期基因含量的方法相对复杂。本文提出了一种使用线性回归计算基因含量的实用方法。该方法不估计基因型概率，但可以假设哈迪-温伯格比例从基因含量中近似估计这些概率。该方法在多个模拟数据集上与其他方法进行了比较，这些数据集是针对具有 1082 头和 907903 头动物的真实牛系谱进行的模拟。在模拟中考虑了不同的等位基因频率（0.4 和 0.2）和缺失基因型的比例（90%、70%和 50%）。模拟表明，与迭代剥除法相比，所提出的方法具有类似的预测基因含量的能力，但它需要的时间更少，对于大型系谱更实用。该方法还应用于大型双用途比利时蓝牛系谱上的牛肌肉生长抑制素基因座的真实数据，该系谱有 235133 头动物。结果表明，该方法可以轻松适应特定的系谱。
