Identification of Genomic Signatures in Bullmastiff Dogs Using Composite Selection Signals Analysis of 23 Purebred Clades.

Simple Summary: Purebred dogs form distinct genetic subpopulations, and there are more than 400 of these recognized by breed clubs around worldwide. Their gene pool is limited by the number of dogs used to develop the breed and how the dogs have been bred. The total makeup of DNA in a breed determines the characteristics that we identify as typical of the breed. However, the limited genetic variation within a breed can also contribute to health issues arising from inherited faulty genes or because of complex interactions of many genes. Many studies have been completed in recent yearsso genetic information is now available for thousands of dogs. Together, this makes dog populations informative subjects for analysis. In this study, we applied a relatively new method which combines three ways to measure variation in the DNA of groups of animals, named Fst, ∆DAF, and XP-EHH, into an index and applied it to the Bullmastiff breed. The method allows us to compare the genomic differences and similarities between groups of individuals from many breeds. We show that there are distinct regions of DNA that are specific to the modern Bullmastiff breed. By focusing on these DNA regions, we can understand some of the characteristics that define the breed and use the information to help us understand how some diseases may be more common in this breed. Dog breeds represent canine sub-populations with distinctive phenotypic features and limited genetic diversity. We have established a resource to study breed-specific genetic diversity. Utilising genetic resources within our laboratory biobank, public domain genotype data and the phylogenetic framework of 23 breed clades, the primary objective for this study was to identify genomic regions that differentiate the Bullmastiff breed. Through application of a composite index analysis (CSS), genomic signatures were identified in Bullmastiffs when compared to the formative breeds, Mastiffs and Bulldogs, and to 22 other breed groups. Significant regions were identified on 15 chromosomes, with the most differentiated regions found on CFA1, CFA9, and CFA18. These regions may reflect genetic drift following establishment of the breed or the effects of selective breeding during development of the modern Bullmastiff. This was supported by analysis of genes from the identified genomic regions, including 458 genes from the multi-clade analysis, which revealed enriched pathways that may be related to characteristic traits and distinct morphology of the breed. The study demonstrates the utility of the CSS method in breed-specific genome analysis and advances our understanding of genetic diversity in Bullmastiff dogs. [ABSTRACT FROM AUTHOR]