Variation of cats under domestication: Genetic assignment of domestic cats to breeds and worldwide random-bred populations

J. D. Kurushima, M. J. Lipinski, B. Gandolfi, L. Froenicke, J. C. Grahn, Robert A Grahn, Leslie A Lyons

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

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 in 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 (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 misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep 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, that is, race.

Original languageEnglish (US)
Pages (from-to)311-324
Number of pages14
JournalAnimal Genetics
Volume44
Issue number3
DOIs
StatePublished - Jun 2013

Fingerprint

domestication
Cats
Single Nucleotide Polymorphism
cats
breeds
Microsatellite Repeats
single nucleotide polymorphism
Population
microsatellite repeats
History
Bayes Theorem
Pets
Pedigree
Esthetics
Genetic Markers
history
Domestication
aesthetics
purebreds
Bayesian theory

Keywords

  • assignment testing
  • Felis catus
  • lineage
  • microsatellite
  • race
  • short tandem repeat
  • single nucleotide polymorphisms

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

Cite this

Variation of cats under domestication : Genetic assignment of domestic cats to breeds and worldwide random-bred populations. / Kurushima, J. D.; Lipinski, M. J.; Gandolfi, B.; Froenicke, L.; Grahn, J. C.; Grahn, Robert A; Lyons, Leslie A.

In: Animal Genetics, Vol. 44, No. 3, 06.2013, p. 311-324.

Research output: Contribution to journalArticle

Kurushima, J. D. ; Lipinski, M. J. ; Gandolfi, B. ; Froenicke, L. ; Grahn, J. C. ; Grahn, Robert A ; Lyons, Leslie A. / Variation of cats under domestication : Genetic assignment of domestic cats to breeds and worldwide random-bred populations. In: Animal Genetics. 2013 ; Vol. 44, No. 3. pp. 311-324.
@article{095be20ca8df4ff1ac904f8af0432373,
title = "Variation of cats under domestication: Genetic assignment of domestic cats to breeds and worldwide random-bred populations",
abstract = "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 in 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 (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 misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep 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, that is, race.",
keywords = "assignment testing, Felis catus, lineage, microsatellite, race, short tandem repeat, single nucleotide polymorphisms",
author = "Kurushima, {J. D.} and Lipinski, {M. J.} and B. Gandolfi and L. Froenicke and Grahn, {J. C.} and Grahn, {Robert A} and Lyons, {Leslie A}",
year = "2013",
month = "6",
doi = "10.1111/age.12008",
language = "English (US)",
volume = "44",
pages = "311--324",
journal = "Animal Genetics",
issn = "0268-9146",
publisher = "Wiley-Blackwell",
number = "3",

}

TY - JOUR

T1 - Variation of cats under domestication

T2 - Genetic assignment of domestic cats to breeds and worldwide random-bred populations

AU - Kurushima, J. D.

AU - Lipinski, M. J.

AU - Gandolfi, B.

AU - Froenicke, L.

AU - Grahn, J. C.

AU - Grahn, Robert A

AU - Lyons, Leslie A

PY - 2013/6

Y1 - 2013/6

N2 - 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 in 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 (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 misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep 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, that is, race.

AB - 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 in 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 (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 misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep 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, that is, race.

KW - assignment testing

KW - Felis catus

KW - lineage

KW - microsatellite

KW - race

KW - short tandem repeat

KW - single nucleotide polymorphisms

UR - http://www.scopus.com/inward/record.url?scp=84876495661&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84876495661&partnerID=8YFLogxK

U2 - 10.1111/age.12008

DO - 10.1111/age.12008

M3 - Article

C2 - 23171373

AN - SCOPUS:84876495661

VL - 44

SP - 311

EP - 324

JO - Animal Genetics

JF - Animal Genetics

SN - 0268-9146

IS - 3

ER -