The Genetic Structure of Domestic Rabbits

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. Levels of nucleotide diversity both within and among breeds were ~0.2%, but only 60% of the diversity present in wild populations from France was captured by domestic rabbits. Despite the recent origin of most breeds, levels of population differentiation were high (F(ST) = 17.9%), but the majority of polymorphisms were shared and thus transferable among breeds. Coalescent simulations suggest that domestication began with a small founding population of less than 1,200 individuals. Taking into account the complex demographic history of domestication with two successive bottlenecks, two loci showed deviations that were consistent with artificial selection, including GPC4, which is known to be associated with growth rates in humans. Levels of diversity were not significantly different between autosomal and X-linked loci, providing no evidence for differential contributions of males and females to the domesticated gene pool. The structure of LD differed substantially within and among breeds. Within breeds, LD extends over large genomic distances. Markers separated by 400 kb typically showed r(2) higher than 0.2, and some LD extended up to 3,200 kb. Much less LD was found among breeds. This advantageous LD structure holds great promise for reducing the interval of association in future mapping studies.

Population structure in Tunisian indigenous rabbit ascertained using molecular information

“…Tunisian rabbit populations exhibit the same genetic diversity compared to Egyptian and Spanish breeds (Ho ranging from 0.36 to 0.48) (Grimal et al, 2012). These results are in general similar to those of previous studies (Bolet et al 2000;Queney et al, 2001;Carneiro et al, 2011) on patrimonial breeds. This finding supports the utility of microsatellites in genetic diversity evaluation of indigenous Tunisian rabbits.…”

Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus

“…The average physical size of these windows was 1.06 Mb. Given that the length scale of linkage disequilibrium (LD) within domestic breeds typically decays to r 2 values between 0.21 and 0.34 at genomic distances of 400 kb (Carneiro et al 2011), this seemed an appropriate window length to avoid elevated homozygosity resulting from demography and chance events. The most extreme window in terms of the occurrence of monomorphic SNPs in dw/dw homozygotes was located at chromosome 4 (chr4):43,668,805-45,210,336 bp ( Figure 2A).…”

Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus)

“…The HBA2 gene is nearly absent in France (we observed the duplication in only 1 out of 63 individuals; Figure 3), and in Iberia the HBA1-HBA2 gene duplication predominates in populations from the hybrid zone, where the allele HBA*3 also occurs at higher frequencies (for example, Ciudad Real, Toledo and Albacete; Figures 1 and 3). Since the domestication of the rabbit was a single event and all domestic rabbits originated from French populations Carneiro et al, 2011), the reported absence of the HBA duplication in domestic rabbits (Cheng et al, 1986) is most likely a common feature of all breeds. This is consistent with surveys of HBA variation in New Zealand White rabbits (n¼24) (Cheng and Hardison, 1988) and in three European breeds (English, Belgian Hare and Fauve de Bourgogne).…”

“…Thus, although the majority of mammalian species possess at least two tandemly duplicated HBA paralogs, the rabbit appears to possess a single HBA gene (Cheng et al, 1986(Cheng et al, , 1987. As this information was based on genomic sequence data from the domesticated rabbit, and as domesticated rabbits represent a small fraction of all genetic diversity present in the species as a whole Carneiro et al, 2011), surveys of natural populations are required to determine whether the unduplicated, single-gene state is fixed in rabbits, or whether there is population-level variation in HBA copy number.…”