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. 2002 Dec;162(4):1863–1873. doi: 10.1093/genetics/162.4.1863

A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus).

J Slate 1, P M Visscher 1, S MacGregor 1, D Stevens 1, M L Tate 1, J M Pemberton 1
PMCID: PMC1462362  PMID: 12524355

Abstract

Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

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Selected References

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  1. Allen Orr H. The genetics of species differences. Trends Ecol Evol. 2001 Jul 1;16(7):343–350. doi: 10.1016/s0169-5347(01)02167-x. [DOI] [PubMed] [Google Scholar]
  2. Almasy L., Blangero J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet. 1998 May;62(5):1198–1211. doi: 10.1086/301844. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Andersson L. Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet. 2001 Feb;2(2):130–138. doi: 10.1038/35052563. [DOI] [PubMed] [Google Scholar]
  4. Band M. R., Larson J. H., Rebeiz M., Green C. A., Heyen D. W., Donovan J., Windish R., Steining C., Mahyuddin P., Womack J. E. An ordered comparative map of the cattle and human genomes. Genome Res. 2000 Sep;10(9):1359–1368. doi: 10.1101/gr.145900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Barendse W., Vaiman D., Kemp S. J., Sugimoto Y., Armitage S. M., Williams J. L., Sun H. S., Eggen A., Agaba M., Aleyasin S. A. A medium-density genetic linkage map of the bovine genome. Mamm Genome. 1997 Jan;8(1):21–28. doi: 10.1007/s003359900340. [DOI] [PubMed] [Google Scholar]
  6. Barton N. H., Keightley P. D. Understanding quantitative genetic variation. Nat Rev Genet. 2002 Jan;3(1):11–21. doi: 10.1038/nrg700. [DOI] [PubMed] [Google Scholar]
  7. Churchill G. A., Doerge R. W. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. doi: 10.1093/genetics/138.3.963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Coulson T. N., Pemberton J. M., Albon S. D., Beaumont M., Marshall T. C., Slate J., Guinness F. E., Clutton-Brock T. H. Microsatellites reveal heterosis in red deer. Proc Biol Sci. 1998 Mar 22;265(1395):489–495. doi: 10.1098/rspb.1998.0321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. George A. W., Visscher P. M., Haley C. S. Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach. Genetics. 2000 Dec;156(4):2081–2092. doi: 10.1093/genetics/156.4.2081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Grosz M. D., MacNeil M. D. Putative quantitative trait locus affecting birth weight on bovine chromosome 2. J Anim Sci. 2001 Jan;79(1):68–72. doi: 10.2527/2001.79168x. [DOI] [PubMed] [Google Scholar]
  11. Hayes B., Goddard M. E. The distribution of the effects of genes affecting quantitative traits in livestock. Genet Sel Evol. 2001 May-Jun;33(3):209–229. doi: 10.1186/1297-9686-33-3-209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Houle D. Comparing evolvability and variability of quantitative traits. Genetics. 1992 Jan;130(1):195–204. doi: 10.1093/genetics/130.1.195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Houle D., Morikawa B., Lynch M. Comparing mutational variabilities. Genetics. 1996 Jul;143(3):1467–1483. doi: 10.1093/genetics/143.3.1467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kearsey M. J., Farquhar A. G. QTL analysis in plants; where are we now? Heredity (Edinb) 1998 Feb;80(Pt 2):137–142. doi: 10.1046/j.1365-2540.1998.00500.x. [DOI] [PubMed] [Google Scholar]
  15. Keightley P. D., Knott S. A. Testing the correspondence between map positions of quantitative trait loci. Genet Res. 1999 Dec;74(3):323–328. doi: 10.1017/s0016672399004176. [DOI] [PubMed] [Google Scholar]
  16. Keller L. F., Jeffery K. J., Arcese P., Beaumont M. A., Hochachka W. M., Smith J. N., Bruford M. W. Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers. Proc Biol Sci. 2001 Jul 7;268(1474):1387–1394. doi: 10.1098/rspb.2001.1607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kruuk L. E., Clutton-Brock T. H., Rose K. E., Guinness F. E. Early determinants of lifetime reproductive success differ between the sexes in red deer. Proc Biol Sci. 1999 Aug 22;266(1429):1655–1661. doi: 10.1098/rspb.1999.0828. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kruuk L. E., Clutton-Brock T. H., Slate J., Pemberton J. M., Brotherstone S., Guinness F. E. Heritability of fitness in a wild mammal population. Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):698–703. doi: 10.1073/pnas.97.2.698. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lai C., Lyman R. F., Long A. D., Langley C. H., Mackay T. F. Naturally occurring variation in bristle number and DNA polymorphisms at the scabrous locus of Drosophila melanogaster. Science. 1994 Dec 9;266(5191):1697–1702. doi: 10.1126/science.7992053. [DOI] [PubMed] [Google Scholar]
  20. Lander E., Kruglyak L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet. 1995 Nov;11(3):241–247. doi: 10.1038/ng1195-241. [DOI] [PubMed] [Google Scholar]
  21. Long A. D., Lyman R. F., Langley C. H., Mackay T. F. Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in Drosophila melanogaster. Genetics. 1998 Jun;149(2):999–1017. doi: 10.1093/genetics/149.2.999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ma R. Z., Beever J. E., Da Y., Green C. A., Russ I., Park C., Heyen D. W., Everts R. E., Fisher S. R., Overton K. M. A male linkage map of the cattle (Bos taurus) genome. J Hered. 1996 Jul-Aug;87(4):261–271. doi: 10.1093/oxfordjournals.jhered.a022999. [DOI] [PubMed] [Google Scholar]
  23. Mackay T. F. Quantitative trait loci in Drosophila. Nat Rev Genet. 2001 Jan;2(1):11–20. doi: 10.1038/35047544. [DOI] [PubMed] [Google Scholar]
  24. Marshall T. C., Slate J., Kruuk L. E., Pemberton J. M. Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol. 1998 May;7(5):639–655. doi: 10.1046/j.1365-294x.1998.00374.x. [DOI] [PubMed] [Google Scholar]
  25. Merilä J, Sheldon BC. Lifetime Reproductive Success and Heritability in Nature. Am Nat. 2000 Mar;155(3):301–310. doi: 10.1086/303330. [DOI] [PubMed] [Google Scholar]
  26. Nuzhdin S. V., Pasyukova E. G., Dilda C. L., Zeng Z. B., Mackay T. F. Sex-specific quantitative trait loci affecting longevity in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9734–9739. doi: 10.1073/pnas.94.18.9734. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Roff D. A., Mousseau T. A. Quantitative genetics and fitness: lessons from Drosophila. Heredity (Edinb) 1987 Feb;58(Pt 1):103–118. doi: 10.1038/hdy.1987.15. [DOI] [PubMed] [Google Scholar]
  28. Seaton George, Haley Chris S., Knott Sara A., Kearsey Mike, Visscher Peter M. QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics. 2002 Feb;18(2):339–340. doi: 10.1093/bioinformatics/18.2.339. [DOI] [PubMed] [Google Scholar]
  29. Shook D. R., Brooks A., Johnson T. E. Mapping quantitative trait loci affecting life history traits in the nematode Caenorhabditis elegans. Genetics. 1996 Mar;142(3):801–817. doi: 10.1093/genetics/142.3.801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Slate J., Coltman D. W., Goodman S. J., MacLean I., Pemberton J. M., Williams J. L. Bovine microsatellite loci are highly conserved in red deer (Cervus elaphus), sika deer (Cervus nippon) and Soay sheep (Ovis aries). Anim Genet. 1998 Aug;29(4):307–315. doi: 10.1046/j.1365-2052.1998.00347.x. [DOI] [PubMed] [Google Scholar]
  31. Slate J., Marshall T., Pemberton J. A retrospective assessment of the accuracy of the paternity inference program CERVUS. Mol Ecol. 2000 Jun;9(6):801–808. doi: 10.1046/j.1365-294x.2000.00930.x. [DOI] [PubMed] [Google Scholar]
  32. Slate J., Pemberton J. M., Visscher P. M. Power to detect QTL in a free-living polygynous population. Heredity (Edinb) 1999 Sep;83(Pt 3):327–336. doi: 10.1038/sj.hdy.6885830. [DOI] [PubMed] [Google Scholar]
  33. Slate Jon, Van Stijn Tracey C., Anderson Rayna M., McEwan K. Mary, Maqbool Nauman J., Mathias Helen C., Bixley Matthew J., Stevens Deirdre R., Molenaar Adrian J., Beever Jonathan E. A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes. Genetics. 2002 Apr;160(4):1587–1597. doi: 10.1093/genetics/160.4.1587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Stone R. T., Keele J. W., Shackelford S. D., Kappes S. M., Koohmaraie M. A primary screen of the bovine genome for quantitative trait loci affecting carcass and growth traits. J Anim Sci. 1999 Jun;77(6):1379–1384. doi: 10.2527/1999.7761379x. [DOI] [PubMed] [Google Scholar]
  35. Veen T., Borge T., Griffith S. C., Saetre G. P., Bures S., Gustafsson L., Sheldon B. C. Hybridization and adaptive mate choice in flycatchers. Nature. 2001 May 3;411(6833):45–50. doi: 10.1038/35075000. [DOI] [PubMed] [Google Scholar]
  36. Visscher P. M., Haley C. S., Heath S. C., Muir W. J., Blackwood D. H. Detecting QTLs for uni- and bipolar disorder using a variance component method. Psychiatr Genet. 1999 Jun;9(2):75–84. doi: 10.1097/00041444-199906000-00005. [DOI] [PubMed] [Google Scholar]
  37. Visscher P. M., Thompson R., Haley C. S. Confidence intervals in QTL mapping by bootstrapping. Genetics. 1996 Jun;143(2):1013–1020. doi: 10.1093/genetics/143.2.1013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Wayne M. L., Hackett J. B., Dilda C. L., Nuzhdin S. V., Pasyukova E. G., Mackay T. F. Quantitative trait locus mapping of fitness-related traits in Drosophila melanogaster. Genet Res. 2001 Feb;77(1):107–116. doi: 10.1017/s0016672300004894. [DOI] [PubMed] [Google Scholar]

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