Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations

Abstract 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 genetically distinct subspecies, Bos indicus and 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 single nucleotide polymorphism (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 to have different effects (unequal variances). 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 very 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 quantitative trait loci (QTL) association mapping in genetically diverse populations.