Genomic analyses of modern dog breeds (original) (raw)

References

• Akey JM, Ruhe AL, Akey DT, Wong AK, Connelly CF, Madeoy J, Nicholas TJ, Neff MW (2010) Tracking footprints of artificial selection in the dog genome. Proc Natl Acad Sci USA 107:1160–1165
  Article PubMed CAS Google Scholar
• Alderton D (2002) Dogs. Dorling Kindersley, Ltd., New York
  Google Scholar
• American Kennel Club (1998) The complete dog book, 19th edn. Howell Book House, New York
  Google Scholar
• American Veterinary Medical Association (2002) U.S. pet ownership and demographics sourcebook, 1st edn. American Veterinary Medical Association, Schaumburg
  Google Scholar
• Awano T, Johnson GS, Wade CM, Katz ML, Johnson GC, Taylor JF, Perloski M, Biagi T, Baranowska I, Long S, March PA, Olby NJ, Shelton GD, Khan S, O’Brien DP, Lindblad-Toh K, Coates JR (2009) Genome-wide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis. Proc Natl Acad Sci USA 106:2794–2799
  Article PubMed CAS Google Scholar
• Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SN, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, de Pardo-Manuel Villena F, Churchill GA (2011) Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 21:1213–1222
  Article PubMed CAS Google Scholar
• Bannasch D, Young A, Myers J, Truvé K, Dickinson P, Gregg J, Davis R, Bongcam-Rudloff E, Webster MT, Lindblad-Toh K, Pedersen N (2010) Localization of canine brachycephaly using an across breed mapping approach. PLoS ONE 5:e9632
  Article PubMed Google Scholar
• Boyko AR, Boyko RH, Boyko CM, Parker HG, Castelhano M, Corey L, Degenhardt JD, Auton A, Hedimbi M, Kityo R, Ostrander EA, Schoenebeck J, Todhunter RJ, Jones P, Bustamante CD (2009) Complex population structure in African village dogs and its implications for inferring dog domestication history. Proc Natl Acad Sci USA 106:13903–13908
  Article PubMed CAS Google Scholar
• 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 Biol 8:e1000451
  Article PubMed Google Scholar
• Brouillette JA, Venta PJ (2002) Within-breed heterozygosity of canine single nucleotide polymorphisms identified by across-breed comparison. Anim Genet 33:464–467
  Article PubMed CAS Google Scholar
• Brown SDM (1996) Genetic variants and strains of the laboratory mouse, 3rd edn. Oxford University Press, New York
  Google Scholar
• Cadieu E, Neff M, Quignon P, Walsh K, Chase K, Parker HG, Vonholdt BM, Rhue A, Boyko A, Byers A, Wong A, Mosher DS, Elkahloun AG, Spady TC, Andre C, Lark KG, Cargill M, Bustamante CD, Wayne RK, Ostrander EA (2009) Coat variation in the domestic dog is governed by variants in three genes. Science 326:150–153
  Article PubMed CAS Google Scholar
• Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325:31–36
  Article PubMed CAS Google Scholar
• Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 38:1251–1260
  Article PubMed CAS Google Scholar
• Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989–2000
  PubMed CAS Google Scholar
• Dodman NH, Karlsson EK, Moon-Fanelli A, Galdzicka M, Perloski M, Shuster L, Lindblad-Toh K, Ginns EI (2010) A canine chromosome 7 locus confers compulsive disorder susceptibility. Mol Psychiatry 15:8–10
  Article PubMed CAS Google Scholar
• Downs LM, Wallin-Håkansson B, Boursnell M, Marklund S, Hedhammar Å, Truvé K, Hübinette L, Lindblad-Toh K, Bergström T, Mellersh CS (2011) A frameshift mutation in Golden Retriever dogs with progressive retinal atrophy endorses SLC4A3 as a candidate gene for human retinal degenerations. PLoS One 6:e21452
  Article PubMed CAS Google Scholar
• Drogemuller C, Karlsson EK, Hytonen MK, Perloski M, Dolf G, Sainio K, Lohi H, Lindblad-Toh K, Leeb T (2008) A mutation in hairless dogs implicates FOXI3 in ectodermal development. Science 321:1462
  Article PubMed Google Scholar
• Farias FHG, Johnson GS, Taylor JF, Giuliano E, Katz ML, Sanders DN, Schnabel RD, McKay SD, Khan S, Gharahkhani P, O’Leary CA, Pettitt L, Forman OP, Boursnell M, McLaughlin B, Ahonen S, Lohi H, Hernandez-Merino E, Gould DJ, Sargan DR, Mellersh C (2010) An ADAMTS17 splice donor site mutation in dogs with primary lens luxation. Invest Ophthalmol Vis Sci 51:4716–4721
  Article PubMed Google Scholar
• Farias FHG, Zeng R, Johnson GS, Wininger FA, Taylor JF, Schnabel RD, McKay SD, Sanders DN, Lohi H, Seppälä EH, Wade CM, Lindblad-Toh K, O’Brien DP, Katz ML (2011) A truncating mutation in ATP13A2 is responsible for adult-onset neuronal ceroid lipofuscinosis in Tibetan terriers. Neurobiol Dis 42:468–474
  Article PubMed CAS Google Scholar
• Federation Cynologique Internationale (2010) Standards and Nomenclature. Available at http://www.fci.be/nomenclature.aspx. Accessed 9 Dec 2011
• Fogle B (1993) ASPCA complete dog care manual. DK Publishing, Inc., New York
  Google Scholar
• Francisco LV, Langston AA, Mellersh CS, Neal CL, Ostrander EA (1996) A class of highly polymorphic tetranucleotide repeats for canine genetic mapping. Mamm Genome 7:359–362
  Article PubMed CAS Google Scholar
• Fredholm M, Wintero AK (1995) Variation of short tandem repeats within and between species belonging to the Canidae family. Mamm Genome 6:11–18
  Article PubMed CAS Google Scholar
• Frome JH (1999, rev. 2004) Staffordshire Bull Terrier. Allenhurst, NJ: Kennel Club Books
• Gao HW, Liang CZ, Zhang YB, Zhu LH (2004) Polymerase chain reaction method to detect canis materials by amplification of species-specific DNA fragment. J AOAC Int 87:1195–1199
  PubMed CAS Google Scholar
• Huson HJ, Parker HG, Runstadler J, Ostrander EA (2010) A genetic dissection of breed composition and performance enhancement in the Alaskan Sled Dog. BMC Genet 11:71
  Article PubMed Google Scholar
• Huson HJ, VonHoldt BM, Rimbault M, Byers AM, Runstadler JA, Parker HG, Ostrander EA (2011) Breed-specific ancestry studies and genome-wide association analysis highlight an association between the MYH9 gene and heat tolerance in Alaskan sprint racing sled dogs. Mamm Genome doi:10.1007/s00335-011-9374-y
• Irion DN, Schaffer AL, Famula TR, Eggleston ML, Hughes SS, Pedersen NC (2003) Analysis of genetic variation in 28 dog breed populations with 100 microsatellite markers. J Hered 94:81–87
  Article PubMed CAS Google Scholar
• Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N, Biagi TM, Patterson N, Pielberg GR, Kulbokas EJ 3rd, Comstock KE, Keller ET, Mesirov JP, von Euler H, Kampe O, Hedhammar A, Lander ES, Andersson G, Andersson L, Lindblad-Toh K (2007) Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 39:1321–1328
  Article PubMed CAS Google Scholar
• Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC (2003) The dog genome: survey sequencing and comparative analysis. Science 301:1898–1903
  Article PubMed Google Scholar
• Koskinen MT (2003) Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog. Anim Genet 34:297–301
  Article PubMed CAS Google Scholar
• Koskinen MT, Bredbacka P (2000) Assessment of the population structure of five Finnish dog breeds with microsatellites. Anim Genet 31:310–317
  Article PubMed CAS Google Scholar
• Lequarre AS, Andersson L, Andre C, Fredholm M, Hitte C, Leeb T, Lohi H, Lindblad-Toh K, Georges M (2011) LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs. Vet J 189:155–159
  Article PubMed Google Scholar
• Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O’Neill B, O’Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803–819
  Article PubMed CAS Google Scholar
• Meurs K, Mauceli E, Lahmers S, Acland G, White S, Lindblad-Toh K (2010) Genome-wide association identifies a deletion in the 3′ untranslated region of Striatin in a canine model of arrhythmogenic right ventricular cardiomyopathy. Hum Genet 128:315–324
  Article PubMed CAS Google Scholar
• Modiano JF, Breen M, Burnett RC, Parker HG, Inusah S, Thomas R, Avery PR, Lindblad-Toh K, Ostrander EA, Cutter GC, Avery AC (2005) Distinct B-cell and T-cell lymphoproliferative disease prevalence among dog breeds indicates heritable risk. Cancer Res 65:5654–5661
  Article PubMed CAS Google Scholar
• Nielen AL, van der Beek S, Ubbink GJ, Knol BW (2001) Population parameters to compare dog breeds: differences between five Dutch purebred populations. Vet Q 23:43–49
  Article PubMed CAS Google Scholar
• Okumura N, Ishiguro N, Nakano M, Matsui A, Sahara M (1996) Intra- and interbreed genetic variations of mitochondrial DNA major non-coding regions in Japanese native dog breeds (Canis familiaris). Anim Genet 27:397–405
  Article PubMed CAS Google Scholar
• Olsson M, Meadows JRS, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar Å, Remmers EF, Andersson L, Ferrer L, Tintle L, Lindblad-Toh K (2011) A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs. PLoS Genet 7:e1001332
  Article PubMed CAS Google Scholar
• Ostrander EA, Sprague GF Jr, Rine J (1993) Identification and characterization of dinucleotide repeat (CA)n markers for genetic mapping in dog. Genomics 16:207–213
  Article PubMed CAS Google Scholar
• Pang JF, Kluetsch C, Zou XJ, Zhang AB, Luo LY, Angleby H, Ardalan A, Ekstrom C, Skollermo A, Lundeberg J, Matsumura S, Leitner T, Zhang YP, Savolainen P (2009) mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Mol Biol Evol 26:2849–2864
  Article PubMed CAS Google Scholar
• Parker HG, Kim LV, Sutter NB, Carlson S, Lorentzen TD, Malek TB, Johnson GS, DeFrance HB, Ostrander EA, Kruglyak L (2004) Genetic structure of the purebred domestic dog. Science 304:1160–1164
  Article PubMed CAS Google Scholar
• Parker HG, Meurs KM, Ostrander EA (2006a) Finding cardiovascular disease genes in the dog. J Vet Cardiol 8:115–127
  Article PubMed Google Scholar
• Parker HG, Sutter NB, Ostrander EA (2006b) Understanding genetic relationships among purebred dogs: the PhyDo project. In: Ostrander EA, Giger U, Lindblad-Toh K (eds) The dog and its genome. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 141–157
  Google Scholar
• Parker HG, Kukekova AV, Akey DT, Goldstein O, Kirkness EF, Baysac KC, Mosher DS, Aguirre GD, Acland GM, Ostrander EA (2007) Breed relationships facilitate fine-mapping studies: a 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds. Genome Res 17:1562–1571
  Article PubMed CAS Google Scholar
• Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA (2009) An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325:995–998
  Article PubMed CAS Google Scholar
• Parker HG, Shearin AL, Ostrander EA (2010) Man’s best friend becomes biology’s best in show: genome analyses in the domestic dog. Annu Rev Genet 44:309–336
  Article PubMed CAS Google Scholar
• Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65:220–228
  Article PubMed CAS Google Scholar
• Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
  PubMed CAS Google Scholar
• Quignon P, Herbin L, Cadieu E, Kirkness EF, Hedan B, Mosher DS, Galibert F, Andre C, Ostrander EA, Hitte C (2007) Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies. PLoS ONE 2:e1324
  Article PubMed Google Scholar
• Quilez J, Short AD, Martinez V, Kennedy LJ, Ollier W, Sanchez A, Altet L, Francino O (2011) A selective sweep of >8 Mb on chromosome 26 in the Boxer genome. BMC Genomics 12:339
  Article PubMed CAS Google Scholar
• Salmon Hillbertz NHC, Isaksson M, Karlsson EK, Hellmen E, Pielberg GR, Savolainen P, Wade CM, von Euler H, Gustafson U, Hedhammar A, Nilsson M, Lindblad-Toh K, Andersson L, Andersson G (2007) Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs. Nat Genet 39:1318–1320
  Article PubMed CAS Google Scholar
• Savolainen P, Zhang YP, Luo J, Lundeberg J, Leitner T (2002) Genetic evidence for an East Asian origin of domestic dogs. Science 298:1610–1613
  Article PubMed CAS Google Scholar
• Savolainen P, Leitner T, Wilton AN, Matisoo-Smith E, Lundeberg J (2004) A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc Natl Acad Sci USA 101:12387–12390
  Article PubMed CAS Google Scholar
• Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316:112–115
  Article PubMed CAS Google Scholar
• Templeton A (2002) Out of Africa again and again. Nature 416:45–51
  Article PubMed CAS Google Scholar
• Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppala EH, Hansen MS, Lawley CT, Karlsson EK, Bannasch D, Vila C, Lohi H, Galibert F, Fredholm M, Haggstrom J, Hedhammar A, Andre C, Lindblad-Toh K, Hitte C, Webster MT (2011) Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet 7:e1002316
  Article PubMed CAS Google Scholar
• Vila C, Savolainen P, Maldonado JE, Amorim IR, Rice JE, Honeycutt RL, Crandall KA, Lundeberg J, Wayne RK (1997) Multiple and ancient origins of the domestic dog. Science 276:1687–1689
  Article PubMed CAS Google Scholar
• Vila C, Maldonado JE, Wayne RK (1999) Phylogenetic relationships, evolution, and genetic diversity of the domestic dog. J Hered 90:71–77
  Article PubMed CAS Google Scholar
• Vila C, Walker C, Sundqvist AK, Flagstad O, Andersone Z, Casulli A, Kojola I, Valdmann H, Halverson J, Ellegren H (2003) Combined use of maternal, paternal and bi-parental genetic markers for the identification of wolf-dog hybrids. Heredity 90:17–24
  Article PubMed CAS Google Scholar
• VonHoldt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, Reynolds A, Bryc K, Brisbin A, Knowles JC, Mosher DS, Spady TC, Elkahloun A, Geffen E, Pilot M, Jedrzejewski W, Greco C, Randi E, Bannasch D, Wilton A, Shearman J, Musiani M, Cargill M, Jones PG, Qian Z, Huang W, Ding ZL, Zhang YP, Bustamante CD, Ostrander EA, Novembre J, Wayne RK (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464:898–902
  Article PubMed CAS Google Scholar
• Wang P, Zangerl B, Werner P, Mauldin E, Casal M (2011) Familial cutaneous lupus erythematosus (CLE) in the German shorthaired pointer maps to CFA18, a canine orthologue to human CLE. Immunogenetics 63:197–207
  Article PubMed Google Scholar
• Wilbe M, Jokinen P, Truve K, Seppala EH, Karlsson EK, Biagi T, Hughes A, Bannasch D, Andersson G, Hansson-Hamlin H, Lohi H, Lindblad-Toh K (2010) Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex. Nat Genet 42:250–254
  Article PubMed CAS Google Scholar
• Wilcox B, Walkowicz C (1995) Atlas of dog breeds of the World, 5th edn. T.F.H. Publications, Neptune City
  Google Scholar
• Wiles-Fone H, Barnes J (1997) The ultimate labrador retriever. Howell Book House, Foster City, CA
  Google Scholar
• Zajc I, Mellersh CS, Sampson J (1997) Variability of canine microsatellites within and between different dog breeds. Mamm Genome 8:182–185
  Article PubMed CAS Google Scholar
• Zeng R, Farias FHG, Johnson GS, McKay SD, Schnabel RD, Decker JE, Taylor JF, Mann CS, Katz ML, Johnson GC, Coates JR, O’Brien DP (2011) A truncated retrotransposon disrupts the GRM1 coding sequence in Coton de Tulear Dogs with Bandera’s Neonatal Ataxia. J Vet Intern Med 25:267–272
  Article PubMed CAS Google Scholar

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