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Abstract
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.
Highlights
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats
In spite of their rapid spread and isolation from the progenitor populations, domestic cats have remained remarkably similar to their felid cousins (Felis silvestris subsp.) in form and behavior[12,14] and these wild populations have remained widespread across the Old World
The final array contains ~63K variants, the highest number of SNPs when compared to the first-generation equine (54.6K), canine (49.6K) and bovine (58.3K) arrays[63,65,66]. This low density array is highly suitable for Mendelian trait analyses, in cat breeds
Summary
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The closest marker with the causative variant in random bred cats requires significantly increasing the number of samples or markers, an association can be detected in Burmese even when reducing the number of samples from 101 to 37 (13 cases and 24 controls); the most significantly associated SNP remained statistically significant (Pvalue = 1.05e−6) after permutations (Pgenome 0.009).
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