Population structure and inbreeding from pedigree analysis of purebred dogs

Genetics

Volumn 179, Issue 1, 2008, Pages 593-601

  Calboli, Federico C F ^a   Sampson, Jeff ^b   Fretwell, Neale ^c   Balding, David J ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b Kennel Club Piccadilly   (United Kingdom)

^c WALTHAM CENTRE FOR PET NUTRITION   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREEDING; CONTROLLED STUDY; DATA BASE; GENETIC VARIABILITY; INBREEDING; NONHUMAN; PEDIGREE; POPULATION STRUCTURE; PRIORITY JOURNAL; PROGENY; UNITED KINGDOM; ANIMAL; BIOLOGICAL MODEL; COMPARATIVE STUDY; DOG; GENETIC DATABASE; GENETICS; POPULATION GENETICS; STATISTICS;

CANIS FAMILIARIS;

ANIMALS; BREEDING; DATABASES, GENETIC; DOGS; GENETICS, POPULATION; GREAT BRITAIN; INBREEDING; MODELS, GENETIC; PEDIGREE; VARIATION (GENETICS);

EID: 52049116143     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.084954     Document Type: Article

References (37)

1. AGARWALA, R., L. G. BIESECKER, K. A. HOPKINS, C. A. FRANCOMANO and A. A. SCHAFFER, 1998 Software for constructing and verifying pedigrees within large genealogies and an application to the old order Amish of Lancaster County. Genome Res. 8: 211-221.
2. BALDING, D. J., 2003 Likelihood-based inference for genetic correlation coefficients. Theor. Popul. Biol. 63: 221-230.
3. BOATTINI, A., F. C. F. CALBOLI, M. J. B. VILLEGAS, P. GUERESI, M. G. FRANCESCHI et al., 2006 Migration matrices and surnames in populations with different isolation patterns: Val di Lima (Italian Apennines), Val di Sole (Italian alps), and La Cabrera (Spain). Am. J. Hum. Biol. 18: 676-690.
4. BOEHMER, L. N., M. F. WU, J. JOHN and J. M. SIEGEL, 2004 Treatment with immunosuppressive and anti-inflammatory agents delays onset of canine genetic narcolepsy and reduces symptom severity. Exp. Neurol. 188: 292-299.
5. BOICHARD, D., 2002 Pedig: a fortran package for pedigree analysis suited for large populations. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, pp. 28-13.
6. BRINKS, J. S., R. T. CLARK and F. J. RICE, 1962 Estimation of genetic trends in beef cattle. J. Anim. Sci. 20: 903.
7. CANNINGS, C., and A. THOMAS, 2007 Inference, simulation and enumeration of pedigrees, pp. 781-807 in Handbook of Statistical Genetics, Ed. 3, edited by D. J. BALDING, M. BISHOP and C. CANNINGS. John Wiley & Sons, Chichester, UK.
8. CARDON, L. R., and L. J. PALMER, 2003 Population stratification and spurious allelic association. Lancet 361: 598-604.
9. CHAPMAN, N. H., A. L. LEUTENEGGER, M. D. BADZIOCH, M. BOGDAN, E. M. CONLON et al., 2001 The importance of connections: joining components of the Hutterite pedigree. Genet. Epidemiol. 21: S230-S235.
10. CHASE, K., D. SARGAN, K. MILLER, E. A. OSTRANDER and K. G. LARK, 2006 Understanding the genetics of autoimmune disease: two loci that regulate late onset Addison's disease in Portuguese Water Dogs. Int. J. Immunogenet. 33: 179-184.
11. CLAYTON, D. G., N. M. WALKER, D. J. SMYTH, R. PASK, J. D. COOPER et al., 2005 Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet. 37: 1243-1246.
12. COLE, J. B., D. E. FRANKE and E. A. LEIGHTON, 2004 Population structure in a colony of dog guides. J. Anim. Sci. 82: 2906-2912.
13. COMSTOCK, K. E., F. LINGAAS, E. F. KIRKNESS, C. HITTE, R. THOMAS et al., 2004 A high-resolution comparative map of canine chromosome 5q14.3-q33 constructed utilizing the 1.5x canine genome sequence. Mamm. Genome 15: 544-551.
14. EXCOFFIER, L., 2007 Analysis of population subdivision, pp. 980-1020 in Handbook of Statistical Genetics, Ed. 3, edited by D. J. BALDING, M. BISHOP and C. CANNINGS. John Wiley & Sons, Chichester, UK.
15. GIRVAN, M., and M. E. J. NEWMAN, 2002 Community structure in social and biological networks. Proc. Natl. Acad. Sci. USA 99: 7821-7826.
16. GIRVAN, M., and M. E. J. NEWMAN, 2004 Finding and evaluating community structure in networks. Phys. Rev. E Stat. Nonlin. Soft Matters Phys. 69: 026113.
17. GUYON, R., S. E. PEARCE-KELLING, C. J. ZEISS, G. M. ACLAND and G. D. AGUIRRE, 2007 Analysis of six candidate genes as potential modifiers of disease expression in canine xlpra1, a model for human x-linked retinitis pigmentosa 3. Mol. Vis. 13: 1094-1105.
18. HURD, J. P., 1983 Comparison of isonymy and pedigree analysis measures in estimating relationships between 3 Nebraska Amish churches in central Pennsylvania. Hum. Biol. 55: 349-355.
19. KARLSSON, E. K., I. BARANOWSKA, N. H. WADE, C. M. HILLBERTZ, M. C. ZODY et al., 2007 Efficient mapping of Mendelian traits in dogs through genome-wide association. Nat. Genet. 39: 1304-1306.
20. KHANNA, C., K. LINDBLAD-TOH, D. VAIL, C. LONDON, P. BERGMAN et al., 2006 The dog as a cancer model. Nat. Biotechnol. 24: 1065-1066.
21. LACY, R. C., 1989 Analysis of founder representation in pedigrees: founders equivalents and founder genome equivalents. Zoo Biol. 8 (2): 111-123.
22. LEROY, G., X. ROGNON, A. VARLET, C. JOFFRIN and E. VERRIER, 2006 Genetic variability in French dog breeds assessed by pedigree data. J. Anim. Breed. Genet. 123: 1-9.
23. LIN, L., J. FARACO, R. LI, H. KADOTANI, W. ROGERS et al., 1999 The sleep disorder canine narcolepsy is caused by a mutation in the hypocretin (orexin) receptor 2 gene. Cell 98: 365-376.
24. LINDBLAD-TOH, K. A., 2007 Trait mapping using a canine SNP array: a model for equine genetics. XV Plant & Animal Genome Conference, p. W101.
25. LINDBLAD-TOH, K., C. M. WADE, T. S. MIKKELSEN, E. K. KARLSSON, D. B. JAFFE et al., 2005 Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819.
26. MARCHINI, J., L. R. CARDON, M. S. PHILLIPS and P. DONNELLY, 2004 The effects of human population structure on large genetic association studies. Nat. Genet. 36: 512-517.
27. MAUL, J. S., N. R. WARNER, S. K. KUWADA, R. W. BURT and L. A. CANNON-ALBRIGHT, 2006 Extracolonic cancers associated with hereditary nonpolyposis colorectal cancer in the Utah population database. Am. J. Gastroenterol. 101: 1591-1596.
28. MEUWISSEN, T. H. E., and Z. LUO, 1992 Computing inbreeding coefficients in large populations. Genet. Sel. Evol. 24: 305-313.
29. NICKERSON, M. L., M. B. WARREN, J. R. TORO, V. MATROSOVA, G. GLENN et al., 2002 Mutations in a novel gene lead to kidney tumors, lung wall defects, and benign tumors of the hair follicle in patients with the birt-hogg-dube syndrome. Cancer Cell 2: 157-164.
30. NORRIS, A. J., D. K. NAYDAN and D. N. WILSON, 2005 Interstitial lung disease in west highland white terriers. Vet. Pathol. 42: 35-41.
31. PARKER, H. G., and E. A. OSTRANDER, 2005 Canine genomics and genetics: running with the pack. PLoS Genet. 1: 507-513.
32. PARKER, H. G., L. V. KIM, N. B. SUTTER, S. CARLSON, T. D. LORENTZEN et al., 2004 Genetic structure of the purebred domestic dog. Science 304: 1160-1164.
33. PUPPO, F., L. TINTLE, A. WONG, I. AKSENTIJEVICH, A. AVERY et al., 2006 The Chinese Shar-Pei dog is a natural model of human autoinflammatory diseases: screening for mutations in the canine mefv, tnfrsfla, cias1 and mvk. Arthritis Rheum. 54: S39.
34. RDEVELOPMENT CORE TEAM, 2007 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
35. SALMON HILLBERTZ, N. H., M. ISAKSSON, E. K. KARLSSON, E. HELLM, G. ROSENGREN PIELBERG et al., 2007 Duplication of fgf3, fgf4, fgf19 and oraov1 causes hair ridge and predisposition to dermoid sinus in ridgeback dogs. Nat. Genet. 38: 1318-1320.
36. THOMPSON, E. A., 1986 Pedigree Analysis in Human Genetics. Johns Hopkins University Press, Baltimore.
37. WRIGHT, S., 1922 Coefficients of inbreeding and relationship. Am. Nat. 56: 330-338.