Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia.
Agresearch Limited, Ruakura Research Centre, Hamilton, 3214, New Zealand.
Heredity (Edinb). 2023 Dec;131(5-6):350-360. doi: 10.1038/s41437-023-00651-4. Epub 2023 Oct 6.
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.
许多对世界农业具有重要意义的植物和动物种群都是亚种杂交的产物。例如，热带和亚热带地区的牛起源于两个亚种，即印度野牛（Bos taurus indicus）和欧洲野牛（Bos taurus taurus）。为了开发这些杂交种群的准确基因组预测，必须找到这些两个亚种的潜在遗传结构的方法。我们提出了一种新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 框架允许来自不同亚种的 SNP 等位基因具有不同的效应。在 B. indicus 和 B. taurus 杂交的综合群体中应用此方法，我们的结果表明，这两个亚种之间存在潜在的基因组差异，而这些效应在不考虑起源亚种效应的多品种基因组评估中无法识别。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 等位基因分配给祖先亚种的起源，我们能够确定四个 SNP 具有很高的包含后验概率，这些 SNP 以前与牛的繁殖力无关，并且与其他物种中与繁殖力相关的基因接近。这些结果表明，单倍型可用于追踪这个杂交群体中亚种的起源，并且结合我们新的贝叶斯分析，可以将亚种 SNP 等位基因分配用于提高遗传多样性群体中 QTL 关联图谱的准确性。
