Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

We thank Dr. Noboru Mizushima for providing the pEGFP-C1-LC3 plasmid and the wild-type and ATG5-knockout MEF cells. We thank Dr. Tamotsu Yoshimori and Dr. Yingyu Chen for the rabbit anti-LC3 polyclonal antibody. Mr. Yabing Liu acknowledged for help with the confocal laser scanning microscopy, and Mrs. Jing Wang is acknowledged for help with the flow cytometry analysis. We thank Dr. Timothy W. McKeithan for suggestions in revising the paper. This work is supported by a key project from the Natural Science Foundation China (No. 30630038) and 973 program project (2006CB910102) awarded to Q. Chen, grants from Tianjin Natural Science Foundation (09JCZDJC21200) to Y. Zhu and from National Basic Research Program (2009CB522002) and the NNSF (30770719) to N. Sui.