11 The Dog Genome: Sequence, Evolution, and Haplotype Structure

Abstract

Man’s best animal friend occupies a very special niche in genomics. Canis familiaris is just the third fully sequenced mammalian genome and the first representative of a new major mammalian clade, Laurasiatheria. (Fig. 1) As is eloquently shown elsewhere in this book, dogs share many common genetic and acquired diseases with their human owners and also much of their environment. In addition, the unique breeding history of the domestic dog makes this species ideally suited for genetic studies. In 2001, an international consortium wrote a white paper and successfully petitioned the National Human Genome Research Institute (NHGRI) for the creation of a high-quality canine sequence to enhance canine disease-gene mapping and mammalian comparative genomics. Large-scale sequencing began in 2003, and, within a year, a high-quality draft sequence of the dog genome was made publicly available.

The assembled dog sequence covers ~99% of the 2.4-Gb genome of a single female boxer. The remarkably high quality of the genome sequence, and the speed at which it was produced, reflected continuing improvements in sequencing and assembly technology since the initiation of the human genome sequence project, which took approximately 10 years to complete. In conjunction with the sequencing, approximately 2.1 million single-nucleotide polymorphisms (SNPs) were identified in the boxer, 10 additional breeds, and 5 other canids, forming the dense, genome-wide marker set necessary for disease-gene mapping and phylogenetic analyses.

Both the genome and the extensive SNP set complement existing genetic resources in the dog community. The dog’s 38 chromosomes, most of which are...