The Genetic Structure of Domestic Rabbits Miguel Carneiro,*,1,2,3 Sandra Afonso,1 Armando Geraldes,4 Herve´ Garreau,5 Gerard Bolet,5 Samuel Boucher,6 Aure´lie Tircazes,5 Guillaume Queney,7 Michael W. Nachman,3 and Nuno Ferrand1,2 1CIBIO, Centro de Investigacxa˜o em Biodiversidade e Recursos Gene´ticos, Campus Agra´rio de Vaira˜o, Vaira˜o 2Departamento de Biologia da Faculdade de Cieˆncias, Universidade do Porto, Porto, Portugal 3Department of Ecology and Evolutionary Biology, University of Arizona 4Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada 5Institut national de la recherche agronomique, UR 631 Station d’ame´lioration ge´ne´tique des animaux, Castanet-Tolosan Cedex, France 6Labovet Conseil, re´seau Cristal, Les Herbiers, France 7Antagene, Wildlife Genetics Laboratory, Limonest, Lyon, France *Corresponding author: E-mail:
[email protected]. Research article Associate editor: Naoko Takezaki Abstract Understanding the genetic structure of domestic species provides a window into the process of domestication and motivates the design of studies aimed at making links between genotype and phenotype. Rabbits exhibit exceptional phenotypic diversity, are of great commercial value, and serve as important animal models in biomedical research. Here, we provide the first comprehensive survey of nucleotide polymorphism and linkage disequilibrium (LD) within and among rabbit breeds. We resequenced 16 genomic regions in population samples of both wild and domestic rabbits and additional 35 fragments in 150 rabbits representing six commonly used breeds. Patterns of genetic variation suggest a single origin of domestication in wild populations from France, supporting historical records that place rabbit domestication in French monasteries.