A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep

Molecular Ecology Resources

Volumn 11, Issue 2, 2011, Pages 314-322

  Miller, J M ^a   Poissant, J ^a   Kijas, J W ^b   Coltman, D W ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b CSIRO   (Australia)

Author keywords

Bighorn sheep; OvineSNP50 BeadChip; Ovis aries; Ovis canadensis; Ovis dalli; Single nucleotide polymorphisms

Indexed keywords

ANIMAL; ARTICLE; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOME; GENOTYPE; MALE; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; WILD ANIMAL;

ANIMALS; ANIMALS, WILD; FEMALE; GENOME; GENOTYPE; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; SHEEP; SHEEP, DOMESTIC;

OVIS ARIES; OVIS CANADENSIS; OVIS DALLI; UNGULATA;

EID: 79751512849     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2010.02918.x     Document Type: Article

References (57)

1. Andersson L (2009) Genome-wide association analysis in domestic animals: a powerful approach for genetic dissection of trait loci. Genetica, 136, 341-349.
2. Backström N, Qvarnström A, Gustafsson L, Ellegren H (2006) Levels of linkage disequilibrium in a wild bird population. Biology Letters, 2, 435-438.
3. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265.
4. Bunch TD, Hoffmann RS, Nadler CF (1999) Cytogenetics and genetics. In: Mountain Sheep of North America (eds Valdez R & Krausman PR). The University of Arizona Press, Tuscon, pp. 263-276.
5. Bunch TD, Wu C, Zhang YP, Wang S (2006) Phylogenetic analysis of snow sheep (Ovis nivicola) and closely related taxa. Journal of Heredity, 97, 21-30.
6. Carlson CS, Eberle MA, Rieder MJ et al. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. The American Journal of Human Genetics, 74, 106-120.
7. Coates BS, Sumerford DV, Miller NJ et al. (2009) Comparative Performance of Single Nucleotide Polymorphism and Microsatellite Markers for Population Genetic Analysis. Journal of Heredity, 100, 556-564.
8. Coltman DW, Festa-Bianchet M, Jorgenson JT, Strobeck C (2002) Age-dependent sexual selection in bighorn rams. Proceedings: Biological Sciences, 269, 165-172.
9. Coltman DW, O'Donoghue P, Jorgenson JT et al. (2003) Undesirable evolutionary consequences of trophy hunting. Nature, 426, 655-658.
10. Coltman DW, O'Donoghue P, Hogg JT, Festa-Bianchet M (2005) Selection and genetic (CO)variance in bighorn sheep. Evolution, 59, 1372-1382.
11. Crestanello B, Pecchioli E, Vernesi C et al. (2009) The Genetic Impact of Translocations and Habitat Fragmentation in Chamois (Rupicapra) spp. Journal of Heredity, 100, 691-708.
12. Dalrymple B, Kirkness E, Nefedov M et al. (2007) Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biology, 8, R152.
13. De La Vega FM, Isaac H, Collins A et al. (2005) The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Research, 15, 454-462.
14. Eberle MA, Rieder MJ, Kruglyak L, Nickerson DA (2006) Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. PLoS Genetics, 2, e142.
15. Feltus FA, Wan J, Schulze SR et al. (2004) An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Research, 14, 1812-1819.
16. Festa-Bianchet M, Coltman DW, Hogg JT, Jorgenson JT (2008) Age-related horn growth, mating tactics, and vulnerability to harvest: why horn curl limits may select for small horns in bighorn sheep. Biennial Symposium of the Northern Wild Sheep and Goat Council, 15, 42-49.
17. Frazer KA, Eskin E, Kang HM et al. (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature, 448, 1050-1053.
18. Gray MM, Granka J, Bustamante CD et al. (2009) Linkage disequilibrium and demographic history of wild and domestic canids. Genetics, 181, 1493-1505.
19. Gregory TR (2010). Animal Genome Size Database.
20. Gregory TR, Nicol JA, Tamm H et al. (2007) Eukaryotic genome size databases. Nucleic Acids Research, 35, D332-D338.
21. Harmegnies N, Farnir F, Davin F et al. (2006) Measuring the extent of linkage disequilibrium in commercial pig populations. Animal Genetics, 37, 225-231.
22. Heifetz EM, Fulton JE, O'Sullivan N et al. (2005) Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations. Genetics, 171, 1173-1181.
23. Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics, 6, 95-108.
24. Hogg JT, Forbes SH (1997) Mating in bighorn sheep: frequent male reproduction via a high-risk "unconventional" tactic. Behavioral Ecology and Sociobiology, 41, 33-48.
25. Iannuzzi L, Meo GP (1995) Chromosomal evolution in bovids: a comparison of cattle, sheep and goat G- and R-banded chromosomes and cytogenetic divergences among cattle, goat and river buffalo sex chromosomes. Chromosome Research, 3, 291-299.
26. Karlsson EK, Baranowska I, Wade CM et al. (2007) Efficient mapping of mendelian traits in dogs through genome-wide association. Nature Genetics, 39, 1321-1328.
27. Khatkar M, Nicholas F, Collins A et al. (2008) Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics, 9, 187.
28. Kijas JW, Townley D, Dalrymple BP et al. (2009) A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE, 4, e4668.
29. Kohn MH, Murphy WJ, Ostrander EA, Wayne RK (2006) Genomics and conservation genetics. Trends in Ecology & Evolution, 21, 629-637.
30. Laurie CC, Nickerson DA, Anderson AD et al. (2007) Linkage disequilibrium in wild mice. PLoS Genetics, 3, e144.
31. Mainguy J, Côté SD, Cardinal E, Houle M (2008) Mating tactics and mate choice in relation to age and social rank in male mountain goats. Journal of Mammalogy, 89, 626-635.
32. McCarthy MI, Abecasis GR, Cardon LR et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature Reviews Genetics, 9, 356-369.
33. McRae AF, McEwan JC, Dodds KG et al. (2002) Linkage disequilibrium in domestic sheep. Genetics, 160, 1113-1122.
34. Meadows J, Chan E, Kijas J (2008) Linkage disequilibrium compared between five populations of domestic sheep. BMC Genetics, 9, 61.
35. Morin PA, Luikart G, Wayne RK, SNP Workshop Grp (2004) SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution, 19, 208-216.
36. Namroud M-C, Beaulieu J, Juge N, Laroche J, Bousquet J (2008) Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Molecular Ecology, 17, 3599-3613.
37. Pertoldi C, Wójcik J, Tokarska M et al. (2010) Genome variability in European and American bison detected using the BovineSNP50 BeadChip. Conservation Genetics, 11, 627-634.
38. Poissant J, Wilson AJ, Festa-Bianchet M, Hogg JT, Coltman DW (2008) Quantitative genetics and sex-specific selection on sexually dimorphic traits in bighorn sheep. Proceedings of the Royal Society B-Biological Sciences, 275, 623-628.
39. Poissant J, Shafer ABA, Davis CS et al. (2009) Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats. Molecular Ecology Resources, 9, 1121-1126.
40. Price AL, Patterson NJ, Plenge RM et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics, 38, 904-909.
41. Purcell S, Neale B, Todd-Brown K et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81, 559-575.
42. R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. 2005.
43. Réale D, Martin J, Coltman DW, Poissant J, Festa-Bianchet M (2009) Male personality, life-history strategies and reproductive success in a promiscuous mammal. Journal of Evolutionary Biology, 22, 1599-1607.
44. Reich DE, Cargill M, Bolk S et al. (2001) Linkage disequilibrium in the human genome. Nature, 411, 199-204.
45. Rezaei HR, Naderi S, Chintauan-Marquier IC et al. (2009) Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae). Molecular Phylogenetics and Evolution, 54, 315-326.
46. Ryynänen HJ, Tonteri A, Vasemägi A, Primmer CR (2007) A comparison of biallelic markers and microsatellites for the estimation of population and conservation genetic parameters in Atlantic salmon (Salmo salar). Journal of Heredity, 98, 692-704.
47. Sacks BN, Louie S (2008) Using the dog genome to find single nucleotide polymorphisms in red foxes and other distantly related members of the Canidae. Molecular Ecology Resources, 8, 35-49.
48. Sechi T, Coltman DW, Kijas JW (2010) Evaluation of 16 loci to examine the cross-species utility of single nucleotide polymorphism arrays. Animal Genetics, 41, 199-202.
49. Slate J, Pemberton JM (2007) Admixture and patterns of linkage disequilibrium in a free-living vertebrate population. Journal of Evolutionary Biology, 20, 1415-1427.
50. Slate J, Gratten J, Beraldi D et al. (2009) Gene mapping in the wild with SNPs: guidelines and future directions. Genetica, 136, 97-107.
51. Stinchcombe JR, Hoekstra HE (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity, 100, 158-170.
52. Stram DO (2004) Tag SNP selection for association studies. Genetic Epidemiology, 27, 365-374.
53. Sutter NB, Eberle MA, Parker HG et al. (2004) Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Research, 14, 2388-2396.
54. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
55. Tozaki T, Hirota K, Hasegawa T, Tomita M, Kurosawa M (2005) Prospects for whole genome linkage disequilibrium mapping in thoroughbreds. Gene, 346, 127-132.
56. VanLiere JM, Rosenberg NA (2008) Mathematical properties of the r2 measure of linkage disequilibrium. Theoretical Population Biology, 74, 130-137.
57. Worley K, Strobeck C, Arthur S et al. (2004) Population genetic structure of North American thinhorn sheep (Ovis dalli). Molecular Ecology, 13, 2545-2556.