Abstract
Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r 2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.
Highlights
A variety of agricultural species was domesticated during the Neolithic revolution, over the course of which specialized breeds emerged
The extended Linkage disequilibrium (LD) documented in other companion animals, such as dog and horse, has proven to be the key for successful genome-wide association studies, especially with relatively low-density DNA arrays [22,55,56,57]
Understanding the extent of LD in cats would undoubtedly aid in performing effective genome-wide association studies
Summary
A variety of agricultural species was domesticated during the Neolithic revolution, over the course of which specialized breeds emerged. The domestic cat, Felis silvestris catus, escaped active and intentional breed development until the 19th century [1,2]. Cat domestication is hypothesized to have originated in the Near East from a still existing wildcat progenitor, Felis silvestris lybica ssp. The newly tamed cats roamed freely around human settlements, randomly breeding as a feral population and occasionally intermingling with the wild progenitor populations [6,7]. As cats entered into a symbiotic relationship with humans, they altered their wild behavior patterns towards that of more tamed companions. After the initial behavior change associated with domestication, most cats have been selected by man mainly for simple aesthetic traits [2], rather than complex behaviors and qualities, such as hunting skills, speed, horsepower, and agriculturally important traits
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