Subspecies-specific BayesR posterior probabilities of inclusion for a composite population of tropically adapted beef heifers

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.

Methods
This dataset is the posterior probabilities of inclusion from the subspecies specific Bayes R analysis using the subspecies specific X-matrix using the Bovine HD array. Each Bovine HD array SNP is repeated 3 times in the file. The subspecies SNP can be differentiated by SNP name, the first SNP is the Bos indicus subspecies SNP, the "_A" SNP is the Bos taurus subspecies SNP and the "_B" SNP is the Bos indicus x Bos taurus subspecies SNP (Bx).