Inbreeding with Low Sequencing Genomic Data

The study and estimation of inbreeding levels is crucial in the study of heredity and genetic disorders. Domestic canines are an effective way to study inbreeding and heredity, as they have been the single oldest species to be domesticated and selectively bred by mankind. Inbreeding levels can be estimated through the inbreeding coefficient (F) with genome sequences that reveal homozygosity. This study aims to calculate inbreeding coefficients in domestic dogs of different breeds using low-coverage gene sequencing data, offering a cost-effective approach to measure genomic inbreeding in populations where high-coverage sequencing may not be feasible. We aimed to gauge inbreeding levels within different dogs based on runs of homozygosity and the inbreeding coefficient. (summary of genome sequencing samples) With the given sequencing data, through the VCF files, on over 90 dogs we assessed the RoH through Plink using the -homozyg tag and the inbreeding coefficient with VCFTools using the -het tag. These two were then regressed against meandepth and compared in order to assess the correlation between the two metrics in terms of estimating inbreeding in dogs. It was found that, one, dogs with higher runs of homozygosity also had higher inbreeding coefficients. And two, that purebred dogs tended to be more inbred vs. dogs that were mutts or mixed breeds. More work needs to be done on connections between assessing inbreeding through these metrics and specific health issues in these dogs as well as possibly expanding the database of dogs used for research.