Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus)

Abstract

Summary The domestic cat (Felis silvestris catus) is a valued companion animal throughout the world. Over 60 different cat breeds are accepted for competition by the cat fancy registries in different countries. Genetic markers, including short tandem repeats and SNPs, are available to evaluate and manage levels of inbreeding and genetic diversity, population and breed structure relationships, and individual identification for forensic and registration purposes. The International Society of Animal Genetics (ISAG) hosts the Applied Genetics in Companion Animals Workshop, which supports the standardization of genetic marker panels and genotyping for the identification of cats via comparison testing. SNP panels have been in development for many species, including the domestic cat. An ISAG approved core panel of SNPs for use in cat identification and parentage analyses is presented. SNPs (n = 121) were evaluated by different university‐based and commercial laboratories using 20 DNA samples as part of the ISAG comparison testing procedures. Different SNP genotyping technologies were examined, including DNA arrays, genotyping‐by‐sequencing and mass spectroscopy, to select a robust and efficient panel of 101 SNPs as the ISAG core panel for cats. The SNPs are distributed across all chromosomes including two on the X chromosome and an XY pseudo‐autosomal sexing marker (zinc‐finger XY; ZFXY). A population study demonstrated that the markers have an average polymorphic information content of 0.354 and a power of exclusion greater than 0.9999. The SNP panel should keep testing affordable while also allowing for the development of additional panels to monitor health, phenotypic traits, hybrid cats and highly inbred cats.

First-degree relationships and genotyping errors deciphered by a high-density SNP array in a Duroc × Iberian pig cross

“…Paternity and maternity identification errors may substantially negatively impact estimated breeding values, genetic trends, inbreeding, and result in the inability to identify truly superior animals in a population [ 16 ]. Furthermore, parentage identification is important to companion animals to evaluate inbreeding and genetic diversity, pedigree structure, and for registration purposes [ 17 ], to free-living animal populations to evaluate population and kinship structure and genetic diversity [ 18 ], and for forensic human identification [ 19 ].…”

“…Although they have been used and are still used widely for parentage verification and identity testing, some problems persist: microsatellite markers are not highly polymorphic in all species, the scoring of markers is not straightforward or automated, and they require a rather large (initial) investment in terms of labor and financial resources [ 23 ]. These problems were largely overcome by the development of SNP markers which have only just been successfully applied in parentage verification in livestock [ 24 ], fish [ 25 ], companion animals [ 17 ], wild animals [ 18 ], and humans [ 19 ].…”

The Revolution of Animal Genomics in Forensic Sciences

“…The employment of biological material from a domestic animal in forensic investigations is becoming frequent [19,20]. One of the first cases in which the analysis of animal DNA has been applied to solve a legal case concerns an episode of illegal cattle purchase that occurred in the Western Pyrenees between France and Spain.…”

Evaluation of parentage testing using single nucleotide polymorphism markers for draft horses in Japan

“…Hundreds of SNPs can now be genotyped at a cost similar to that of STR genotyping (Tokarska et al, 2009). SNP genotyping is more conducive to robotic automation than STR genotyping, thereby increasing testing (de Groot et al, 2021). Millions of SNPs have been identified for horses (Tozaki et al, 2021; Wade et al, 2009), and Hirota et al (2010) and Holl et al (2017) developed parentage testing panels based on these SNPs.…”