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 o..., 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)., , # Subspecies-specific BayesR Posterior Probability of Inclusion

[https://doi.org/10.5061/dryad.q2bvq83rk](https://doi.org/10.5061/dryad.q2bvq83rk)

Th warburton_subspecies_bayesr dataset contains the BayesR posterior probabilities for subspecies specific SNP from the subspecies BayesR analysis using a customised X-matrix. This analysis has been designed in tropical beef populations which consist of two subspecies, *Bos indicus* and *Bos taurus.* Haplotypes are assigned to a subspecies of origin and each SNP that falls within the haplotype window is assigned to that subspecies of origin. As there are two haplotypes per haplotype window, SNP can be classified into homozygous *Bos indicus* (Bi), homozygous *Bos taurus* (Bt) and a composite *Bos indicus x Bos taurus* (Bx) depending upon the ancestral origins of both haplotypes within the haplotype window. A customised X-matrix was developed that had the dimensions *nanim x 3nsnp* where *nanim* is the number of animals and *3nsnp* is 3 time...