Genome Wide Copy Number Variation in the Canine Genome

The domestic dog (Canis lupus familiaris) is one of the most phenotypically diverse species in existence.  This diversity has led to numerous studies identifying variants responsible for different dog phenotypes (Baranowska 2014, Cadieu 2009).  Many of these studies focus on single nucleotide polymorphisms (SNPS) or are genome-wide association studies (GWAS).  Our study focuses on the effects of copy number variants. Copy number variants (CNVs) are duplications or deletions of genomic segments that range from 50 bps to megabasepairs and vary among individuals within a species (Conrad 2010). Since CNVs can change gene structure and dosage (Zhang 2009) they may have greater effects on phenotype than single nucleotide polymorphisms (SNPs). However due to their tendency to be located near segmental duplications they are difficult to identify. The improvement of sequence analysis software is overcoming this issue however. The Complementary Sequence Variant Detection (CoSVarD) pipeline (Bickhart unpublished) is a two part program which allows researchers to identify SNPs, insertions, deletions (INDELs), and CNVs.  In our study we attempt to identify CNVs that affect phenotype in dogs, wolves, coyotes, and jackals.  We will then determine copy number estimates throughout the genome as well as identify breed and species specific CNVs.