A simple genetic architecture underlies morphological variation in dogs

Adam R. Boyko, Pascale Quignon, Lin Li, Jeffrey J. Schoenebeck, Jeremiah D. Degenhardt, Kirk E. Lohmueller, Keyan Zhao, Abra Brisbin, Heidi G. Parker, Bridgett M. vonHoldt, Michele Cargill, Adam Auton, Andy Reynolds, Abdel G. Elkahloun, Marta Castelhano, Dana S. Mosher, Nathan B. Sutter, Gary S. Johnson, John Novembre, Melissa J. Hubisz & 4 others Adam Siepel, Robert K. Wayne, Carlos D. Bustamante, Elaine A. Ostrander

Research output: Contribution to journalArticle

232 Citations (Scopus)

Abstract

Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

Original languageEnglish (US)
Pages (from-to)49-50
Number of pages2
JournalPLoS Biology
Volume8
Issue number8
DOIs
StatePublished - Aug 2010
Externally publishedYes

Fingerprint

Dogs
Mammals
dogs
Museums
Polymorphism
Body Size
Bone
Nucleotides
Genes
breeds
body size
dog breeds
phenotypic variation
genomics
Canidae
Quantitative Trait Loci
quantitative traits
genotyping
single nucleotide polymorphism
chromosome mapping

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)

Cite this

Boyko, A. R., Quignon, P., Li, L., Schoenebeck, J. J., Degenhardt, J. D., Lohmueller, K. E., ... Ostrander, E. A. (2010). A simple genetic architecture underlies morphological variation in dogs. PLoS Biology, 8(8), 49-50. https://doi.org/10.1371/journal.pbio.1000451

A simple genetic architecture underlies morphological variation in dogs. / Boyko, Adam R.; Quignon, Pascale; Li, Lin; Schoenebeck, Jeffrey J.; Degenhardt, Jeremiah D.; Lohmueller, Kirk E.; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G.; vonHoldt, Bridgett M.; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G.; Castelhano, Marta; Mosher, Dana S.; Sutter, Nathan B.; Johnson, Gary S.; Novembre, John; Hubisz, Melissa J.; Siepel, Adam; Wayne, Robert K.; Bustamante, Carlos D.; Ostrander, Elaine A.

In: PLoS Biology, Vol. 8, No. 8, 08.2010, p. 49-50.

Research output: Contribution to journalArticle

Boyko, AR, Quignon, P, Li, L, Schoenebeck, JJ, Degenhardt, JD, Lohmueller, KE, Zhao, K, Brisbin, A, Parker, HG, vonHoldt, BM, Cargill, M, Auton, A, Reynolds, A, Elkahloun, AG, Castelhano, M, Mosher, DS, Sutter, NB, Johnson, GS, Novembre, J, Hubisz, MJ, Siepel, A, Wayne, RK, Bustamante, CD & Ostrander, EA 2010, 'A simple genetic architecture underlies morphological variation in dogs', PLoS Biology, vol. 8, no. 8, pp. 49-50. https://doi.org/10.1371/journal.pbio.1000451
Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE et al. A simple genetic architecture underlies morphological variation in dogs. PLoS Biology. 2010 Aug;8(8):49-50. https://doi.org/10.1371/journal.pbio.1000451
Boyko, Adam R. ; Quignon, Pascale ; Li, Lin ; Schoenebeck, Jeffrey J. ; Degenhardt, Jeremiah D. ; Lohmueller, Kirk E. ; Zhao, Keyan ; Brisbin, Abra ; Parker, Heidi G. ; vonHoldt, Bridgett M. ; Cargill, Michele ; Auton, Adam ; Reynolds, Andy ; Elkahloun, Abdel G. ; Castelhano, Marta ; Mosher, Dana S. ; Sutter, Nathan B. ; Johnson, Gary S. ; Novembre, John ; Hubisz, Melissa J. ; Siepel, Adam ; Wayne, Robert K. ; Bustamante, Carlos D. ; Ostrander, Elaine A. / A simple genetic architecture underlies morphological variation in dogs. In: PLoS Biology. 2010 ; Vol. 8, No. 8. pp. 49-50.
@article{5e2ac74a2a3a44f69e1668d1aa9f6794,
title = "A simple genetic architecture underlies morphological variation in dogs",
abstract = "Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.",
author = "Boyko, {Adam R.} and Pascale Quignon and Lin Li and Schoenebeck, {Jeffrey J.} and Degenhardt, {Jeremiah D.} and Lohmueller, {Kirk E.} and Keyan Zhao and Abra Brisbin and Parker, {Heidi G.} and vonHoldt, {Bridgett M.} and Michele Cargill and Adam Auton and Andy Reynolds and Elkahloun, {Abdel G.} and Marta Castelhano and Mosher, {Dana S.} and Sutter, {Nathan B.} and Johnson, {Gary S.} and John Novembre and Hubisz, {Melissa J.} and Adam Siepel and Wayne, {Robert K.} and Bustamante, {Carlos D.} and Ostrander, {Elaine A.}",
year = "2010",
month = "8",
doi = "10.1371/journal.pbio.1000451",
language = "English (US)",
volume = "8",
pages = "49--50",
journal = "PLoS Biology",
issn = "1544-9173",
publisher = "Public Library of Science",
number = "8",

}

TY - JOUR

T1 - A simple genetic architecture underlies morphological variation in dogs

AU - Boyko, Adam R.

AU - Quignon, Pascale

AU - Li, Lin

AU - Schoenebeck, Jeffrey J.

AU - Degenhardt, Jeremiah D.

AU - Lohmueller, Kirk E.

AU - Zhao, Keyan

AU - Brisbin, Abra

AU - Parker, Heidi G.

AU - vonHoldt, Bridgett M.

AU - Cargill, Michele

AU - Auton, Adam

AU - Reynolds, Andy

AU - Elkahloun, Abdel G.

AU - Castelhano, Marta

AU - Mosher, Dana S.

AU - Sutter, Nathan B.

AU - Johnson, Gary S.

AU - Novembre, John

AU - Hubisz, Melissa J.

AU - Siepel, Adam

AU - Wayne, Robert K.

AU - Bustamante, Carlos D.

AU - Ostrander, Elaine A.

PY - 2010/8

Y1 - 2010/8

N2 - Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

AB - Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

UR - http://www.scopus.com/inward/record.url?scp=77956800100&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77956800100&partnerID=8YFLogxK

U2 - 10.1371/journal.pbio.1000451

DO - 10.1371/journal.pbio.1000451

M3 - Article

VL - 8

SP - 49

EP - 50

JO - PLoS Biology

JF - PLoS Biology

SN - 1544-9173

IS - 8

ER -