Genetic linkage map of a wild genome: Genomic structure, recombination and sexual dimorphism in bighorn sheep

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Poissant, Jocelyn ^a   Hogg, John T ^b   Davis, Corey S ^a   Miller, Joshua M ^a   Maddox, Jillian F ^c   Coltman, David W ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b Montana Conservation Science Institute   (United States)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; CENTROMERE; CONTIG MAPPING; CONTROLLED STUDY; DOMESTIC ANIMAL; DOMESTICATION; FEMALE; GENE STRUCTURE; GENETIC CONSERVATION; GENETIC DISTANCE; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETIC TRAIT; GENETIC VARIABILITY; MALE; MICROSATELLITE MARKER; NONHUMAN; ORTHOLOGY; PEDIGREE ANALYSIS; PLACENTAL MAMMALS; SEX DIFFERENCE; SHEEP; SPECIES DIFFERENCE; SYNTENY; TELOMERE; X CHROMOSOME; ANIMAL; CHROMOSOME MAP; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; GENOME; GENOTYPE; PEDIGREE; POPULATION DYNAMICS; SEXUAL DEVELOPMENT;

EUTHERIA; OVIS; OVIS ARIES; OVIS CANADENSIS;

ANIMALS; CENTROMERE; CHROMOSOME MAPPING; FEMALE; GENETIC LINKAGE; GENETIC MARKERS; GENOME; GENOTYPE; MALE; PEDIGREE; POLYMORPHISM, GENETIC; POPULATION DYNAMICS; RECOMBINATION, GENETIC; SEX CHARACTERISTICS; SHEEP, BIGHORN; SHEEP, DOMESTIC; TELOMERE;

EID: 77957115670     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-524     Document Type: Article

References (63)

1. Slate J. Quantitative trait locus mapping in natural populations: progress, caveats and future directions. Mol Ecol 2005, 14:363-380. 10.1111/j.1365-294X.2004.02378.x, 15660931.
2. Slate J. Robustness of linkage maps in natural populations: a simulation study. Proc R Soc B 2008, 275:695-702. 10.1098/rspb.2007.0948, 2596837, 18211883.
3. Slate J, Visscher PM, MacGregor S, Stevens D, Tate ML, Pemberton JM. A genome scan for quantitative trait loci in a wild population of Red Deer (Cervus elaphus). Genetics 2002, 162:1863-1873. 1462362, 12524355.
4. Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM. Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of soay sheep (Ovis aries). Genetics 2006, 173:1-17. 10.1534/genetics.106.057141, 1461452, 16723419.
5. Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM. Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population. Evolution 2007, 953:1403-1416.
6. Beraldi D, McRae AF, Gratten J, Pilkington JG, Slate J, Visscher PM, Pemberton JM. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries). Int J Parasitol 2007, 37:121-129. 10.1016/j.ijpara.2006.09.007, 17067607.
7. Gratten J, Beraldi D, Lowder BV, McRay AF, Vissher PM, Pemberton JM, Slate J. Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep. Proc R Soc B 2007, 274:619-626. 10.1098/rspb.2006.3762, 2197217, 17254985.
8. Johnston SE, Beraldi D, McRae AF, Pemberton JM, Slate J. Horn type and horn length genes map to the same chromosomal region in Soay sheep. Heredity 2010, 104:196-205. 10.1038/hdy.2009.109, 19690581.
9. Gratten J, Wilson AJ, McRae AF, Beraldi D, Visscher PM, Pemberton JM, Slate J. A localized negative genetic correlation constrains microevolution of coat color in wild sheep. Science 2008, 319:318-320. 10.1126/science.1151182, 18202287.
10. Backström N, Qvarnstrom A, Gustafsson L, Ellegren H. Levels of linkage disequilibrium in a wild bird population. Biol Lett 2006, 2:435-438. 10.1098/rsbl.2006.0507, 1686206, 17148424.
11. Slate J, Pemberton J. Admixture and patterns of linkage disequilibrium in a free-living vertebrate population. J Evol Biol 2007, 20:1415-1427. 10.1111/j.1420-9101.2007.01339.x, 17584236.
12. Slate J, Santure AW, Feulner PGD, Brown EA, Ball AD, Johnston SE, Gratten J. Genome mapping in intensively studied wild vertebrate populations. Trends Genet 2010, 26:275-284. 10.1016/j.tig.2010.03.005, 20444518.
13. Valdez R, Krausman PR. Mountain sheep of North America. 1999, Tucson: University of Arizona Press.
14. Hogg JT, Forbes SH, Steele BM, Luikart G. Genetic rescue of an insular population of large mammals. Proc R Soc B 2006, 273:1491-1499. 10.1098/rspb.2006.3477, 1560318, 16777743.
15. Poissant J, Wilson AJ, Festa-Bianchet M, Hogg JT, Coltman DW. Quantitative genetics and sex-specific selection on sexually dimorphic traits in bighorn sheep. Proc R Soc B 2008, 275:623-628. 10.1098/rspb.2007.1361, 2596849, 18211870.
16. Poissant J, Shafer ABA, Davis CS, Mainguy J, Hogg JT, Coté SD, Coltman DW. Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats. Mol Ecol Resour 2009, 9:1121-1126.
17. Coltman DW. Molecular ecological approaches to studying the evolutionary impact of selective harvesting in wildlife. Mol Ecol 2008, 17:221-235. 10.1111/j.1365-294X.2007.03414.x, 18173501.
18. Bunch TD, Wu C, Zhang Y-P, Wang S. Phylogenetic analysis of snow sheep (Ovis nivicola) and closely related taxa. J Hered 2006, 97:21-30. 10.1093/jhered/esi127, 16267166.
19. Bunch TD, Hoffmann RS, Nadler CF. Cytogenetics and genetics. Mountain sheep of North America 1999, 263-276. Tucson: The University of Arizona Press, Valdez R, Krausman PR.
20. Delgadillo C, Mejía V, Berruecos V, Vásquez P. Morphological study of chromosomes of Bighorn sheep (Ovis canadensis), Domestic sheep (Ovis aries) and their crosses. Vet Mex 2003, 34:27-37.
21. Pontius JU, Mullikin JC, Smith DR, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, O'Brien SJ. Initial sequence and comparative analysis of the cat genome. Genome Res 2007, 17:1675-1689. 10.1101/gr.6380007, 2045150, 17975172.
22. Maddox JF, Cockett NE. An update on sheep and goat linkage maps and other genomic resources. Small Rumin Res 2007, 70:4-20.
23. Tucker EM, Denis B, Kilgour L. Blood genetic marker studies of a sheep-goat hybrid and its back-cross offspring. Anim Genet 1989, 20:179-186. 10.1111/j.1365-2052.1989.tb00855.x, 2757269.
24. McRae AF, Beraldi D. Examination of a region showing linkage map discrepancies across sheep breeds. Mamm Genome 2006, 17:346-353. 10.1007/s00335-005-0087-y, 16596456.
25. Burt A, Bell G. Mammalian chiasma frequencies as a test of two theories of recombination. Nature 1987, 326:803-805. 10.1038/326803a0, 3574451.
26. Coop G, Przeworski M. An evolutionary view of human recombination. Nat Rev Genet 2007, 8:23-34. 10.1038/nrg1947, 17146469.
27. Ross-Ibarra J. The evolution of recombination under domestication: a test of two hypotheses. Am Nat 2004, 163:105-112. 10.1086/380606, 14767840.
28. Dumont BL, Payseur BA. Evolution of the genomic rate of recombination in mammals. Evolution 2008, 62:276-294. 10.1111/j.1558-5646.2007.00278.x, 18067567.
29. Maddox JF, Davies KP, Crawford AM, Hulme DJ, Vaiman D, Cribiu EP, Freking BA, Beh KJ, Cockett NE, Kang N, Riffkin CD, Drinkwater R, Moore SS, Dodds KG, Lumsden JM, van Stijn TC, Phua SH, Adelson DL, Burkin HR, Broom JE, Buitkamp J, Cambridge L, Cushwa WT, Gerard E, Galloway SM, Harrison B, Hawken RJ, Hiendleder S, Henry HM, Medrano JF, Paterson KA, Schibler L, Stone RT, van Hest B. An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res 2001, 11:1275-1289. 10.1101/gr.GR-1350R, 311104, 11435411.
30. Cox A, Ackert-Bicknell CL, Dumont BL, Ding Y, Tzenova Bell J, Brockmann GA, Wergedal JE, Bult C, Paigern B, Flint J, Tsaih S-W, Churchill GA, Broman KW. A new standard genetic map for the laboratory mouse. Genetics 2009, 182:1335-1344. 10.1534/genetics.109.105486, 2728870, 19535546.
31. Lenormand T, Dutheil J. Recombination difference between sexes: a role for haploid selection. PLoS Biol 2005, 3:e63. 10.1371/journal.pbio.0030063, 1044830,1044830, 15736976.
32. Miles L, Isberg S, Glenn T, Lance S, Dalzell P, Thomson P, Moran C. A genetic linkage map for the saltwater crocodile (Crocodylus porosus). BMC Genomics 2009, 10:339. 10.1186/1471-2164-10-339, 2907706, 19640266.
33. Singer A, Perlman H, Yan Y, Walker C, Corley-Smith G, Brandhorst B, Postlethwait J. Sex-specific recombination rates in zebrafish (Danio rerio). Genetics 2002, 160:649-657. 1461993, 11861568.
34. Ihara N, Takasuga A, Mizoshita K, Takeda H, Sugimoto M, Mizoguchi Y, Hirano T, Itoh T, Watanabe T, Reed KM, Snelling WM, Kappes SM, Beattie CW, Bennett GL, Sugimoto Y. A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites. Genome Res 2004, 14:1987-1998. 10.1101/gr.2741704, 524423, 15466297.
35. Dumont BL, Broman K, Payseur BA. Variation in genomic recombination rates among heterogeneous stock mice. Genetics 2009, 182:1345-1349. 10.1534/genetics.109.105114, 2728871, 19535547.
36. Poissant J, Wilson AJ, Coltman DW. Sex-specific genetic variance and the evolution of sexual-dimorphism: a systematic review of cross-sex genetic correlations. Evolution 2010, 64:97-107. 10.1111/j.1558-5646.2009.00793.x, 19659596.
37. Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng SHS, Graber JH, Broman KW, Petkov PM. The recombinational anatomy of a mouse chromosome. PLoS Genet 2008, 4:e1000119. 10.1371/journal.pgen.1000119, 2440539, 18617997.
38. Broman KW, Murray JC, Sheffield VC, White RL, Weber JL. Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet 1998, 63:861-869. 10.1086/302011, 1377399, 9718341.
39. Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GAT, Gabriel SB, Reich D, Donnelly P, Altshuler D. Comparison of fine-scale recombination rates in humans and chimpanzees. Science 2005, 308:107-111. 10.1126/science.1105322, 15705809.
40. Ptak SE, Hinds DA, Koehler K, Nickel B, Patil N, Ballinger DG, Przeworski M, Frazer KA, Paabo S. Fine-scale recombination patterns differ between chimpanzees and humans. 2005, 37:429-434.
41. Lynn A, Ashley T, Hassold T. Variation in human meiotic recombination. Annu Rev Genomics Hum Genet 2004, 5:317-349. 10.1146/annurev.genom.4.070802.110217, 15485352.
42. Miller JM, Poissant J, Kijas JW, Coltman DW, . the International Sheep Genomics Consortium A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Mol Ecol Res 2010, the International Sheep Genomics Consortium.
43. International Sheep Genomics Consortium. , http://www.sheephapmap.org/
44. Réale D, Martin J, Coltman DW, Poissant J, Festa-Bianchet M. Male personality, life-history strategies and reproductive success in a promiscuous mammal. J Evol Biol 2009, 22:1599-1607. 10.1111/j.1420-9101.2009.01781.x, 19555442.
45. Stinchcombe JR, Hoekstra HE. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 2007, 100:158-170. 10.1038/sj.hdy.6800937, 17314923.
46. Luikart G, Pilgrim K, Visty J, Ezenwa VO, Schwartz MK. Candidate gene microsatellite variation is associated with parasitism in wild bighorn sheep. Biol Lett 2008, 4:228-231. 10.1098/rsbl.2007.0633, 2429941, 18270161.
47. Coltman DW, O'Donoghue P, Jorgenson JT, Hogg JT, Strobeck C, Festa-Bianchet M. Undesirable consequences of trophy hunting. Nature 2003, 426:655-658. 10.1038/nature02177, 14668862.
48. Marshall TC, Slate J, Kruuk LEB, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 1998, 7:639-655. 10.1046/j.1365-294x.1998.00374.x, 9633105.
49. O'Connell JR, Weeks DE. PedCheck: A program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet 1998, 63:259-266. 10.1086/301904, 1377228, 9634505.
50. Kinghorn BP. Pedigree Viewer - a graphical utility for browsing pedigreed data sets. 5th World Congress on Genetics Applied to Livestock Production 1994, 85-86. University of Guelph, Canada, Smith C, Gavora JS, Benkel B, Chesuais J, Fairfull W, Gibson JP.
51. Australian Sheep Gene Mapping Web Site. , http://rubens.its.unimelb.edu.au/~jillm/jill.htm
52. Maudet C, Beja-Pereira A, Zeyl E, Nagash H, Kence A, Ozut D, Biju-Duval M-P, Boolormaa S, Coltman DW, Taberlet P, Luikart G. A standard set of polymorphic microsatellites for threatened mountain ungulates (Caprini, Artiodactyla). Mol Ecol Notes 2004, 4:49-55.
53. Georges M, Massey J. Polymorphic DNA markers in Bovidae (World Intellectual Property Org., Geneva). 1992, WO Publication No 92/13102.
54. Ede AJ, Pierson CA, Crawford AM. Ovine microsatellites at the OarCP34, OarCP38, OarCP43, OarCP49, OarCP73, OarCP79 and OarCP99. Anim Genet 1995, 26:130-131. 10.1111/j.1365-2052.1995.tb02656.x, 7733504.
55. Stone RT, Pulido JC, Duyk GM, Kappes SM, Keele JW, Beattie CW. A small-insert bovine genomic library highly enriched for microsatellite repeat sequences. Mamm Genome 1995, 6:714-724. 10.1007/BF00354294, 8563170.
56. Dieringer D, Schlötterer C. Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 2003, 3:167-169.
57. Green P, Falls K, Crooks S. Documentation for CRI-MAP, version 2.4. 1990, St-Louis: Washington University.
58. Liu X, Grosz M. Linkage mapping software user's guide. 2006, St-Louis: Monsanto Company.
59. Kosambi DD. The estimation of map distance from recombination values. Ann Eugen 1944, 12:172-175.
60. Sokal RR, Rohlf FJ. Biometry. The principles and practice of statistics in biological research. 1995, New York: W. H. Freeman and Company, Third.
61. Bohonak AJ. RMA. Software for reduced major axis regression. 2004, http://www.bio.sdsu.edu/pub/andy/RMA.html
62. Lovich JE, Gibbons JW. A review of techniques for quantifying sexual size dimorphism. Growth Dev Aging 1992, 56:269-281.
63. Fairbairn DJ. Introduction: the enigma of sexual size dimorphism. Sex, size and gender roles. Evolutionary studies of sexual dimorphism 2007, 1-15. Oxford: Oxford University Press, Fairbairn DJ, Blanckenhorn WU, Székely T.