Many of the world’s agriculturally important plant and animal populations consist of hybrids of subspecies. Cattle in tropical and sub-tropical regions for example, originate from two subspecies, Bos taurus indicus (Bos indicus) and Bos taurus taurus (Bos taurus). Methods to derive the underlying genetic architecture for these two subspecies are essential to develop accurate genomic predictions in these hybrid populations. We propose a novel method to achieve this. First, we use haplotypes to assign SNP alleles to ancestral subspecies of origin in a multi-breed and multi-subspecies population. Then we use a BayesR framework to allow SNP alleles originating from the different subspecies differing effects. Applying this method in a composite population of B. indicus and B. taurus hybrids, our results show that there are underlying genomic differences between the two subspecies, and these effects are not identified in multi-breed genomic evaluations that do not account for subspecies of origin effects. The method slightly improved the accuracy of genomic prediction. More significantly, by allocating SNP alleles to ancestral subspecies of origin, we were able to identify four SNP with high posterior probabilities of inclusion that have not been previously associated with cattle fertility and were close to genes associated with fertility in other species. These results show that haplotypes can be used to trace subspecies of origin through the genome of this hybrid population and, in conjunction with our novel Bayesian analysis, subspecies SNP allele allocation can be used to increase the accuracy of QTL association mapping in genetically diverse populations.

世界上许多重要的农业动植物种群都由亚种的杂交组成。例如，热带和亚热带地区的牛起源于两个亚种：牛( Bos indicus )和牛(Bos taurus)。推导这两个亚种的潜在遗传结构的方法对于在这些杂交种群中进行准确的基因组预测至关重要。我们提出了一种新颖的方法来实现这一目标。首先，我们使用单倍型将 SNP 等位基因分配给多品种和多亚种群体中的祖先亚种。然后我们使用BayesR框架来让源自不同亚种的SNP等位基因产生不同的影响。将这种方法应用于B. indicus和B. taurus杂交种的复合种群，我们的结果表明，两个亚种之间存在潜在的基因组差异，并且在不考虑亚种的多品种基因组评估中没有发现这些影响。原点效应。该方法略微提高了基因组预测的准确性。更重要的是，通过将 SNP 等位基因分配给起源的祖先亚种，我们能够识别出具有高后验概率的 4 个 SNP，这些 SNP 以前未与牛的生育力相关，并且与其他物种的生育力相关基因接近。这些结果表明，单倍型可用于通过该杂交群体的基因组追踪亚种起源，并且与我们新颖的贝叶斯分析相结合，亚种 SNP 等位基因分配可用于提高遗传多样性群体中 QTL 关联作图的准确性。