Lessons learned from the dog genome

Trends in Genetics

Volumn 23, Issue 11, 2007, Pages 557-567

  Wayne, Robert K ^a   Ostrander, Elaine A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL BEHAVIOR; BACKCROSSING; BREEDING; CHROMOSOME ANALYSIS; DNA SEQUENCE; DOG; DOMESTICATION; GENE LINKAGE DISEQUILIBRIUM; GENE POOL; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; GENOTYPE PHENOTYPE CORRELATION; HAPLOTYPE; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; PHENOTYPE; PHYLOGENY; POPULATION GENETICS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BASE SEQUENCE; BREEDING; DOGS; EVOLUTION, MOLECULAR; GENOME; LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; PHENOTYPE; PHYLOGENY; VARIATION (GENETICS); WOLVES;

CANIS FAMILIARIS; CANIS LUPUS;

EID: 35748957135     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2007.08.013     Document Type: Review

References (91)

1. In: American Kennel Club Staff (Ed). The Complete Dog Book (1998), Howell Book House
2. In: Stockard C.R. (Ed). The genetic and endocrinic basis for differences in form and behavior, as elucidated by studies of contrasted pure-line dog breeds and their hybrids (1941), The Wistar Institute of Anatomy and Biology
3. In: Scott J.P., and Fuller J.L. (Eds). Genetics and the Social Behaviour of the Dog (1965), University of Chicago Press
4. Ostrander E.A., and Wayne R.K. The canine genome. Genome Res. 15 (2005) 1706-1716
5. Pollinger J.P., et al. Selective sweep mapping of genes with large phenotypic effects. Genome Res. 15 (2005) 1809-1819
6. Stinchcombe J.R., and Hoekstra H.E. Combining population genomics and quantitative genetics: approaches for finding the genes underlying ecologically important traits. Heredity (2007). www.nature.com 10.1038/sj.hdy.6800937
7. Sutter N.B., et al. A single ancient IGF1 allele causes small size in dogs. Science 316 (2007) 112-115
8. Kohn M.H., et al. Genomics and conservation genetics. Trends Ecol. Evol. 21 (2006) 629-637
9. Wayne R.K., et al. Molecular systematics of the Canidae. Syst. Biol. 46 (1997) 622-653
10. Lindblad-Toh K., et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438 (2005) 803-819
11. Geffen E., et al. Phylogenetic relationships of the fox-like canids: mitochondrial DNA restriction fragment, site and Cytochrome b sequence analyses. J. Zool. Lond. 228 (1992) 27-39
12. Bardeleben C., et al. A molecular phylogeny of the Canidae based on six nuclear loci. Mol. Phylogenet. Evol. 37 (2005) 815-831
13. Bardeleben C., et al. Isolation and molecular evolution of the selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) genes in the dog family, Canidae. Mol. Biol. Evol. 22 (2005) 347-359
14. Wayne R.K., et al. Molecular and biochemical evolution of the Carnivora. In: Gittleman J.L. (Ed). Carnivore Behavior, Ecology and Evolution (1989), Cornell University Press 465-494
15. Wayne R.K., and Morin P.A. Conservation genetics in the new molecular age. Front Ecol. Environ. 2 (2004) 89-97
16. Kukekova A.V., et al. A meiotic linkage map of the silver fox, aligned and compared to the canine genome. Genome Res. 17 (2007) 387-399
17. Aguilar A., et al. High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 3490-3494
18. Edwards S.V., and Hedrick P.W. Evolution and ecology of MHC molecules: from genomics to sexual selection. Trends Ecol. Evol. 13 (1998) 305-311
19. Seddon J.M., et al. SNPs in ecological and conservation studies: A test in the Scandinavian wolf population. Mol. Ecol. 14 (2005) 503-511
20. Morin P.A., et al. SNPs in ecology, evolution and conservation. Trends Ecol. Evol. 19 (2004) 208-216
21. Savolainen P., et al. Genetic evidence for an East Asian origin of domestic dogs. Science 298 (2002) 1610-1613
22. Wayne R.K., et al. Genetic analysis of dog domestication. In: Zeder M.E., et al. (Ed). Documenting Domestication: New Genetic and Archaeological Paradigms (2005), Smithsonian Institution Press 279-293
23. Leonard J.A., et al. Ancient DNA evidence for old world origin of new world dogs. Science 298 (2002) 1613-1616
24. Sablin M.V., and Khlopachev G.A. The earliest ice age dogs: Evidence from Eliseevichi. Curr. Anthropol. 43 (2002) 795-799
25. Bjornerfeldt S., et al. Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res. 16 (2006) 990-994
26. Vila C., et al. Genes of domestic mammals augmented by backcrossing with wild ancestors. Trends Genet. 21 (2005) 214-218
27. Angles J.M., et al. Frequency and distribution of alleles of canine MHC-II DLA-DQB1, DLA-DQA1 and DLA-DRB1 in 25 representative American Kennel Club breeds. Tissue Antigens 66 (2005) 173-184
28. Runstadler J.A., et al. Dog leucocyte antigen class II diversity and relationships among indigenous dogs of the island nations of Indonesia (Bali), Australia and New Guinea. Tissue Antigens 68 (2006) 418-426
29. Schmutz S.M., et al. Agouti sequence polymorphisms in coyotes, wolves and dogs suggest hybridization. J. Hered. 98 (2007) 351-355
30. Verardi A., et al. Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis. Mol. Ecol. 15 (2006) 2845-2855
31. Parker H.G., et al. Genetic structure of the purebred domestic dog. Science 304 (2004) 1160-1164
32. Irion D.N., et al. Analysis of genetic variation in 28 dog breed populations with 100 microsatellite markers. J. Hered. 94 (2003) 81-87
33. Irion D.N., et al. Genetic variation analysis of the Bali street dog using microsatellites. BMC Genet 6 (2005) 6
34. Puja I.K., et al. The Kintamani dog: genetic profile of an emerging breed from Bali. Indonesia. J. Hered. 96 (2005) 854-859
35. Leonard J.A., et al. From wild wolf to domestic dog. In: Ostrander E.A., Giger U., and Lindblad-Toh K. (Eds). The Dog and Its Genome (2005), Cold Spring Harbor Monograph Series 95-118
36. Savolainen P., et al. A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 12387-12390
37. Bannasch D.L., et al. Y chromosome haplotype analysis in purebred dogs. Mamm. Genome 16 (2005) 273-280
38. Natanaelsson C., et al. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery. BMC Genet. 7 (2006) 45
39. Sundqvist A.-K., et al. Unequal contribution of sexes in the origin of dog breeds. Genetics 172 (2006) 1121-1128
40. Wayne R.K. Cranial morphology of domestic and wild canids: the influence of development on morphological change. Evolution 40 (1986) 243-261
41. Wayne R.K. Limb morphology of domestic and wild canids: the influence of development on morphologic change. J. Morphol. 187 (1986) 301-319
42. Svartberg K., and Forkman B. Personality traits in the domestic dog (Canis familiaris). Appl. Anim. Behav. Sci. 79 (2002) 133-155
43. Ostrander E.A., et al. Canine genetics comes of age. Trends Genet. 16 (2000) 117-124
44. Sutter N.B., and Ostrander E.A. Dog star rising: the canine genetic system. Nat. Rev. Genet. 5 (2004) 900-910
45. In: Wilcox B., and Walkowicz C. (Eds). Atlas of Dog Breeds of the World. 5th edn (1995), T.F.H. Publications
46. Koskinen M.T. Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog. Anim. Genet. 34 (2003) 297-301
47. Parker, H.G. et al. Breed relationships facilitate fine mapping studies: A 7.8-kb deletion segregates with collie eye anomaly across multiple dog breeds. Genome Res, DOI:10.1101/gr.6772807 (www.genome.org)
48. Neff M.W., et al. Breed distribution and history of canine mdr1-1Δ, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 11725-11730
49. Hyun C., et al. Prospects for whole genome linkage disequilibrium mapping in domestic dog breeds. Mamm. Genome 14 (2003) 640-649
50. Lou X.Y., et al. The extent and distribution of linkage disequilibrium in a multi-hierarchic outbred canine pedigree. Mamm. Genome 14 (2003) 555-564
51. Sutter N.B., et al. Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Res. 14 (2004) 2388-2396
52. Wade C., et al. The dog genome: Sequence, evolution and haplotype structure. In: Ostrander E.A., Giger U., and Lindblad-Toh K. (Eds). The Dog and Its Genome (2006), Cold Spring Harbor Monograph Series 179-208
53. Switonski M., et al. The dog genome map and its use in mammalian comparative genomics. J. Appl. Genet. 45 (2004) 195-214
54. Parker H.G., and Ostrander E.A. Canine genomics and genetics: running with the pack. PLoS Genet. 1 (2005) e58
55. Safra N., et al. Linkage analysis with an interbreed backcross maps Dalmatian hyperuricosuria to CFA03. Mamm. Genome 17 (2006) 340-345
56. van De Sluis B., et al. Identification of a new copper metabolism gene by positional cloning in a purebred dog population. Hum. Mol. Genet. 11 (2002) 165-173
57. Chase K., et al. Understanding the genetics of autoimmune disease: two loci that regulate late onset Addison's disease in Portuguese water dogs. Int. J. Immunogenet. 33 (2006) 179-184
58. Acland G.M., et al. Linkage analysis and comparative mapping of canine progressive rod-cone degeneration (prcd) establishes potential locus homology with retinitis pigmentosa (RP17) in humans. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 3048-3053
59. Acland G.M., et al. A novel retinal degeneration locus identified by linkage and comparative mapping of canine early retinal degeneration. Genomics 59 (1999) 134-142
60. Sidjanin D.J., et al. Canine CNGB3 mutations establish cone degeneration as orthologous to the human achromatopsia locus ACHM3. Hum. Mol. Genet. 11 (2002) 1823-1833
61. Lingaas F., et al. A mutation in the canine BHD gene is associated with hereditary multifocal renal cystadenocarcinoma and nodular dermatofibrosis in the German Shepherd dog. Hum. Mol. Genet. 12 (2003) 3043-3053
62. Lin L., et al. The sleep disorder canine narcolepsy is caused by a mutation in the hypocretin (orexin) receptor 2 gene. Cell 98 (1999) 365-376
63. Lingaas F., et al. Genetic markers linked to neuronal ceroid lipofuscinosis in English setter dogs. Anim. Genet. 29 (1998) 371-376
64. Lohi H., et al. Expanded repeat in canine epilepsy. Science 307 (2005) 81
65. Chase K., et al. Bilaterally asymmetric effects of quantitative trait loci (QTLs): QTLs that affect laxity in the right versus left coxofemoral (hip) joints of the dog (Canis familiaris). Am. J. Med. Genet. A. 124 (2004) 239-247
66. Chase K., et al. Genetic regulation of osteoarthritis: A QTL regulating cranial and caudal acetabular osteophyte formation in the hip joint of the dog (Canis familiaris). Am. J. Med. Genet. A. 135 (2005) 334-335
67. Todhunter R.J., et al. Quantitative trait loci for hip dysplasia in a cross-breed canine pedigree. Mamm. Genome 16 (2005) 720-730
68. Clark L.A., et al. Linkage analysis and gene expression profile of pancreatic acinar atrophy in the German Shepherd Dog. Mamm. Genome 16 (2005) 955-962
69. Murgia C., et al. Clonal origin and evolution of a transmissible cancer. Cell 126 (2006) 477-487
70. vonHoldt B.M., and Ostrander E.A. The singular history of a canine transmissible tumor. Cell 126 (2006) 445-447
71. Bostanci A. Wildlife biology. A devil of a disease. Science 307 (2005) 1035
72. Sargan D.R. IDID: inherited diseases in dogs: Web-based information for canine inherited disease genetics. Mamm. Genome 15 (2004) 503-506
73. Cordaux R., and Batzer M.A. Teaching an old dog new tricks: SINEs of canine genomic diversity. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 1157-1158
74. Clark L.A., et al. Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 1376-1381
75. Lark K.G., et al. Genetic architecture of the dog: sexual size dimorphism and functional morphology. Trends Genet. 22 (2006) 537-544
76. Kharlamova A.V., et al. Genetic regulation of canine skeletal traits: trade-offs between the hind limbs and forelimbs in the fox and dog. Integr. Comp. Biol. 47 (2007) 373-381
77. Haworth K.E., et al. Canine TCOF1; cloning, chromosome assignment and genetic analysis in dogs with different head types. Mamm. Genome 12 (2001) 622-629
78. Young A.E., et al. Deletions in the COL10A1 gene are not associated with skeletal changes in dogs. Mamm. Genome 17 (2006) 761-768
79. Mosher D.S., et al. A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs. PLoS Genetics 3 (2007) e79
80. Fondon III J.W., and Garner H.R. Molecular origins of rapid and continuous morphological evolution. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 18058-18063
81. Laidlaw J., et al. Elevated basal slippage mutation rates among the canidae. J. Hered. 98 (2007) 452-460
82. Fondon III J.W., and Garner H.R. Detection of length-dependent effects of tandem repeat alleles by 3-D geometric deomposition of craniofacial variation. Dev. Genes Evol. 217 (2007) 79-85
83. Chase K., et al. Genetic basis for systems of skeletal quantitative traits: principal component analysis of the canid skeleton. Proc. Natl. Acad Sci. U. S. A. 99 (2002) 9930-9935
84. Hare B., et al. The domestication of social cognition in dogs. Science 298 (2002) 1634-1636
85. Reisner I.R., et al. National survey of owner-directed aggression in English Springer Spaniels. J. Am. Vet. Med. Assoc. 227 (2005) 1594-1603
86. Saetre P., et al. From wild wolf to domestic dog: gene expression changes in the brain. Brain Res. Mol. Brain Res. 126 (2004) 198-206
87. Linberg J., et al. Reduced expression of TAC1, PENK and SOCS2 in Hcrtr-2 mutated narcoleptic dog brain. BMC Neurosci. 8 (2007) 34
88. Saetre P., et al. The genetic contribution to canine personality. Genes Brain Behav. 5 (2006) 240-248
89. Ito H., et al. Allele frequency distribution of the canine dopamine receptor D4 gene exon III and I in 23 breeds. J. Vet. Med. Sci. 66 (2004) 815-820
90. Trut L.N., et al. An experiment on fox domestication and debatable issues of evolution of the dog. Genetika 40 (2004) 794-807
91. Lindberg J., et al. Selection for tameness has changed brain gene expression in silver foxes. Curr. Biol. 15 (2005) R915-R916