The Feline SNP Array: Features and Utility

The development of high throughput SNP genotyping technologies has radically changed the genetic dissection of simple and complex traits in human as well as in cats.  SNP arrays permit genome-wide population based analyses at very low costs.  Eight diverse cat breeds and populations were re-sequenced for SNP discovery in the cat genome.  The discovered SNPs were used to develop an Illumina high-density array with ~63,000 SNPs.  A comprehensive database composed of over 3000 genotyped cats representing over 40 distinct breeds and populations was used to investigate the array’s features and utility.  The first aim was to investigate the efficiency of the array in various population-based analyses. As a measure of the efficiency of the array, the following were addressed: (1) SNP remapping to their proper location in the latest feline genome assembly (8.0), (2) SNP genotyping rates in over two thousand cats, (3) SNP Mendelian errors rates using 86 trios, and lastly (4) general population specific summary statistics in 48 distinct cat populations.  The second aim was to examine the array’s utility and power to detect feline population structure and associations with various traits of interest. The genotypes of 2161 individuals cats (48 populations) were used to determine (1) genetic structure among cat populations, (2) extent of linkage disequilibrium in various populations, and (3) power of the array to reveal regions of association with (dominant and recessive) traits/diseases in small cat breeds and in random bred populations.