12 SINEs of Canine Genomic Diversity

Abstract

Different breeds of dogs clearly display characteristic phenotypes, such as morphologies, behaviors, and susceptibilities to disease. Because of the extreme variation of these phenotypes between breeds, the dog species provides us with a valuable model system to identify the specific genetic variations that underlie these traits. Until recently, such studies have been hampered by the limited amount of available genomic sequence data from dogs. However, this situation has now changed dramatically, due to the survey-sequencing of a poodle genome, the generation of a draft sequence for a boxer genome, and extensive sampling of sequence data from the genomes of multiple breeds of dogs and wild canids (Kirkness et al. 2003; K. Lindblad-Toh et al., in prep.). In combination, these sequence data provide us with considerable insight into the extent of genomic variation between individual dogs and into the best strategies for identifying those variations that are responsible for traits of interest. In common with humans, the most frequent genomic sequence variations between individual dogs are single-nucleotide polymorphisms (SNPs) and variable numbers of tandem repeats (VNTRs). A distinct type of polymorphism that is much more frequent in dogs than in humans is caused by variable insertions of short interspersed elements (SINEs; Kirkness et al. 2003). Here, we consider the potential phenotypic consequences of these variable SINE insertions. In addition, we consider their utility as abundant, evenly distributed polymorphisms that can be used to better understand relationships between dog breeds and between domesticated dogs and wild canids. INFLUENCE OF SINEs ON EUKARYOTIC