Variation of cats under domestication: genetic assignment of domestic cats to breeds and worldwide random‐bred populations

Abstract

Summary Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also the historical origins of common household cats. The cat fancy is a relatively new institution with over 85% of its 40–50 breeds arising only in the past 75 years, primarily through selection on single-gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker-based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (accuracy single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the mis-assigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multi-step assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, i.e. race.

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

“…Five known wildcats by domestic cat hybrids obtained in captivity were included in the analyses (Pierpaoli et al, 2003). Domestic cats (F. s. catus, n = 139) living in regions sympatric to the wildcats but in urban areas were also genotyped (Table 1; Lipinski et al, 2008;Kurushima et al, 2012). DNA from tissue samples was extracted as described by Pop is the population designation used in the analyses (codes used in Figure 1).…”

“…Buccal swabs from domestic cats from Cyprus were obtained from the Cyprus Malcolm Cat Sanctuary and were prepared as previously described (Kurushima et al, 2012). DNA from putative European wildcats and captive bred hybrids was whole-genome-amplified according to the manufacturer's recommendations using the REPLI-g Midi Kit (Qiagen Inc, Hilden, Germany).…”

“…Most of the SNPs (134) were randomly selected from Kurushima et al (2012), including 48 in intragenic regions, and were opportunistically applied to this study. Two phenotypic SNPs, associated with cat coat colors, TYR (Siamese-points) and TYRP1 (brown), were also examined (Lyons et al, 2005a, b).…”

“…Additional 22 SNPs in intragenic regions were genotyped, including the following: (i) nine that revealed at least one polymorphic position between European wildcat and domestic cats (Johnson et al, 2006); (ii) one for which high variability was known among domestic cats (CCR2; Esteves et al, 2007); (iii) one considered to be leopard cat (CAT; Prionailurus bengalensis) species-specific; (iv) four on the X chromosome; and (v) seven randomly selected intragenic SNPs (Supplementary Table 1). The later seven randomly intragenic SNPs were selected at the same time and with the same criteria as Kurushima et al (2012). Briefly, SNPs were previously selected from the 1.9 × coverage of the Abyssinian cat (Pontius et al, 2007), being heterozygous in the Abyssinian, within nonrepetitive regions and dispersed across the chromosomes.…”

“…Finally, each SNP had a call rate 480% and a minor allele frequency 45% across the entire data set, which is considered the inherent error rate in the assay efficiency. Golden Gate Assay amplification and BeadXpress reads were performed following the manufacturer's protocol (Illumina Inc, San Diego, CA, USA) on 50-500 ng of DNA or whole-genome-amplified product (Kurushima et al, 2012) …”