Skip to main content

Quantitative Trait Loci Mapping

  • Protocol
Book cover Osteoporosis

Abstract

This chapter presents current methods for mapping quantitative trait loci (QTLs) in natural populations especially in humans. We discussed the experimental designs for QTL mapping, traditional methods adopted such as linkage mapping approaches and methods for linkage disequilibrium (LD) mapping. Multiple traits and interaction analysis are also outlined. The application of modern genomic approaches, which mainly exploit the microarray technology, into QTL mapping was detailed. The latter are very recent protocols and are less developed than linkage and association methods at present. The main focus of this chapter is technical issues although statistical issues are also covered to certain extent. Finally, we summarize the limitations of the current QTL approaches and discuss the solutions to certain problems.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. 1. Falconer, D. S., Mackay, T. F. C. (1996) Introduction to Quantitative Genetics. Longman, Essex, UK.

    Google Scholar 

  2. 2. Geldermann, H. (1975) Investigations on inheritance of quantitative characters in animals by gene markers. I. Methods. Theor Appl Genet 46, 319–330.

    Article  Google Scholar 

  3. 3. Elston, R. C., Buxbaum, S., Jacobs, K. B., et al. (2000) Haseman and Elston revisited. Genet Epidemiol 19, 1–17.

    Article  CAS  PubMed  Google Scholar 

  4. 4. Hill, W. G. (1981) Estimation of effective population size from data on linkage disequilibrium. Genet Res 38, 209–216.

    Article  Google Scholar 

  5. 5. Hill, W. J., Robertson, A. (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38, 226–231.

    Article  Google Scholar 

  6. 6. Patil, N., Berno, A. J., Hinds, D. A., et al. (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719–1723.

    Article  CAS  PubMed  Google Scholar 

  7. 7. Gabriel, S. B., Schaffner, S. F., Nguyen, H., et al. (2002) The structure of haplotype blocks in the human genome. Science 296, 2225–2229.

    Article  CAS  PubMed  Google Scholar 

  8. 8. Williams, J. T., Van Eerdewegh, P., Almasy, L., et al. (1999) Joint multipoint linkage analysis of multivariate qualitative and quantitative traits. I. Likelihood formulation and simulation results. Am J Hum Genet 65, 1134–1147.

    Article  CAS  PubMed  Google Scholar 

  9. 9. Amos, C. I., Elston, R. C., Bonney, G. E., et al. (1990) A multivariate method for detecting genetic linkage, with application to a pedigree with an adverse lipoprotein phenotype. Am J Hum Genet 47, 247–254.

    CAS  PubMed  Google Scholar 

  10. 10. Schork, N. J. (1993) Extended multipoint identity-by-descent analysis of human quantitative traits: efficiency, power, and modeling considerations. Am J Hum Genet 53, 1306–1319.

    CAS  PubMed  Google Scholar 

  11. 11. Almasy, L., Dyer, T. D., Blangero, J. (1997) Bivariate quantitative trait linkage analysis: plei-otropy versus co-incident linkages. Genet Epidemiol 14, 953–958.

    Article  CAS  PubMed  Google Scholar 

  12. 12. Moore, J. H. (2003) The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56, 73–82.

    Article  PubMed  Google Scholar 

  13. 13. Jansen, R. C., Nap, J. P. (2001) Genetical genomics: the added value from segregation. Trends Genet 17, 388–391.

    Article  CAS  PubMed  Google Scholar 

  14. 14. DeCook, R., Lall, S., Nettleton, D., et al. (2006) Genetic regulation of gene expression during shoot development in Arabinosis. Genetics 172, 1155–1164.

    Article  CAS  Google Scholar 

  15. 15. Schadt, E. E., Monks, S. A., Drake, T. A., et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297–302.

    Article  CAS  PubMed  Google Scholar 

  16. 16. Yaguchi, H., Togawa, K., Moritani, M., et al. (2005) Identification of candidate genes in the type 2 diabetes modifier locus using expression QTL. Genomics 85, 591–599.

    Article  CAS  PubMed  Google Scholar 

  17. 17. Hirschhorn, J. N., Daly, M. J. (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6, 95–108.

    Article  CAS  PubMed  Google Scholar 

  18. 18. Herbert, A., Gerry, N. P., McQueen, M. B., et al. (2006) A common genetic variant is associated with adult and childhood obesity. Science 312, 279–283.

    Article  CAS  PubMed  Google Scholar 

  19. 19. John, S., Shephard, N., Liu, G., et al. (2004) Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites. Am J Hum Genet 75, 54–64.

    Article  CAS  PubMed  Google Scholar 

  20. 20. Klein, R. J., Zeiss, C., Chew, E. Y. , et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308, 385–389.

    Article  CAS  PubMed  Google Scholar 

  21. 21. Maraganore, D. M., de Andrade, M., Lesnick, T. G., et al. (2005) High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet 77, 685–693.

    Article  CAS  PubMed  Google Scholar 

  22. 22. Namkung, J., Kim, Y., Park, T. (2005) Whole-genome association studies of alcoholism with loci linked to schizophrenia susceptibility. BMC Genet 6, S9.

    Article  PubMed  Google Scholar 

  23. 23. Spinola, M., Meyer, P., Kammerer, S., et al. (2006) Association of the PDCD5 locus with lung cancer risk and prognosis in smokers. J Clin Oncol 24, 1672–1678.

    Article  CAS  PubMed  Google Scholar 

  24. 24. Weaver, T. A. (2000) High-throughout SNP discovery and typing for genome-wide genetic analysis. A Trends Guide 20, 136–142.

    Google Scholar 

  25. 25. Syvanen, A. C. (2005) Toward genome-wide SNP genotyping. Nat Genet 37, S5–10.

    Article  PubMed  Google Scholar 

  26. 26. Stoll, M., Kwitek-Black, A. E., Cowley, A. W., et al. (2000) New target regions for human hypertension via comparative genomics. Genome Res 10, 473–482.

    Article  CAS  PubMed  Google Scholar 

  27. 27. Lynch, M., Walsh, B. (1998) Genetics and Analysis of Quantitative Traits. Sinauer Associates,Sunderland, MA.

    Google Scholar 

  28. 28. Haseman, J. K., Elston, R. C. (1972) The investigation of linkage between a quantitative trait and a marker locus. Behav Genet 2, 3–19.

    Article  CAS  PubMed  Google Scholar 

  29. 29. Almasy, L., Blangero, J. (1998) Multipoint quantitative-trait linkage analysis in general pedi grees. Amer J Hum Genet 62, 1198–1211.

    Article  CAS  PubMed  Google Scholar 

  30. 30. George, A. W., Visscher, P. M., Haley, C. S. (2000) Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach. Genetics 156, 2081–2092.

    CAS  PubMed  Google Scholar 

  31. 31. Slate, J., Pemberton, J. M., Visscher, P. M. (1999) Power to detect QTL in a free-living pulig-enous population. Heredity 83, 327–336.

    Article  PubMed  Google Scholar 

  32. 32. Amos, C. I., Elston, R. C. (1989) Robust methods for the detection of genetic linkage for quantitative data from pedigrees. Genet Epidemiol 6, 349–360.

    Article  CAS  PubMed  Google Scholar 

  33. 33. Fulker, D. W., Cardon, L. R. (1994) A sib-pair approach to interval mapping of quantitative trait loci. Am J Hum Genet 54, 1092–1103.

    CAS  PubMed  Google Scholar 

  34. 34. Tiwari, H. K., Elston, R. C. (1997) Linkage of multilocus components of variance to polymor phic markers. Ann Hum Genet 61, 253–261.

    CAS  PubMed  Google Scholar 

  35. 35. Amos, C. I. (1994) Robust variance-components approach for assessing genetic linkage in pedigrees. Am J Hum Genet 54, 535–543.

    CAS  PubMed  Google Scholar 

  36. 36. Devlin, B., Roeder, K., Wasserman, L. (2001) Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 60, 155–166.

    Article  CAS  PubMed  Google Scholar 

  37. 37. Devlin, B., Roeder, K., Bacanu, S. A. (2001) Unbiased methods for population-based associa tion studies. Genet Epidemiol 21, 273–284.

    Article  CAS  PubMed  Google Scholar 

  38. 38. Pritchard, J. K., Rosenberg, N. A. (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65, 220–228.

    Article  CAS  PubMed  Google Scholar 

  39. 39. Schaid, D. J. (1998) Transmission disequilibrium, family controls, and great expectations. Am J Hum Genet 63, 935–941.

    Article  CAS  PubMed  Google Scholar 

  40. 40. Benjamini, Y. A. H. Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc Series B 57, 289–300.

    Google Scholar 

  41. 41. McIntyre, L. M., Martin, E. R., Simonsen, K. L., et al. (2000) Circumventing multiple testing: a multilocus Monte Carlo approach to testing for association. Genet Epidemiol 19, 18–29.

    Article  CAS  PubMed  Google Scholar 

  42. 42. Boomsma, D. I., Dolan, C. V. (1998) A comparison of power to detect a QTL in sib-pair data using multivariate phenotypes, mean phenotypes, and factor scores. Behav Genet 28,329–340.

    Article  CAS  PubMed  Google Scholar 

  43. 43. Blangero, J., Almasy, L. (1997) Multipoint oligogenic linkage analysis of quantitative traits.Genet Epidemiol 14, 959–964.

    Article  CAS  PubMed  Google Scholar 

  44. 44. Cockerham, C. C., Zeng, Z. B. (1996) Design III with marker loci. Genetics 143,1437–1456.

    CAS  PubMed  Google Scholar 

  45. 45. Thomas, D., Xie, R., Gebregziabher, M. (2004) Two-Stage sampling designs for gene associa tion studies. Genet Epidemiol 27, 401–414.

    Article  PubMed  Google Scholar 

  46. 46. Kruglyak, L., Daly, M. J., Reeve-Daly, M. P., et al. (1996) Parametric and nonparametric link age analysis: a unified multipoint approach. Am J Hum Genet 58, 1347–1363.

    CAS  PubMed  Google Scholar 

  47. 47. Abecasis, G. R., Cherny, S. S., Cookson, W. O., et al. (2002) Merlin: rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30, 97–101.

    Article  CAS  PubMed  Google Scholar 

  48. 48. Gudbjartsson, D. F., Jonasson, K., Frigge, M. L., et al. (2000) Allegro, a new computer pro gram for multipoint linkage analysis. Nat Genet 25, 12–13.

    Article  CAS  PubMed  Google Scholar 

  49. 49. Shmulewitz, D., Heath, S. C., Blundell, M. L., et al. (2006) Linkage analysis of quantitative traits for obesity, diabetes, hypertension, and dyslipidemia on the island of Kosrae, Federated States of Micronesia. Proc Natl Acad Sci U S A 103, 3502–3509.

    Article  CAS  PubMed  Google Scholar 

  50. 50. Abecasis, G. R., Cardon, L. R., Cookson, W. O. (2000) A general test of association for quan titative traits in nuclear families. Am J Hum Genet 66, 279–292.

    Article  CAS  PubMed  Google Scholar 

  51. 51. Horvath, S., Xu, X., Laird, N. M. (2001) The family based association test method: strategies for studying general genotype: phenotype associations. Eur J Hum Genet 9, 301–306.

    Article  CAS  PubMed  Google Scholar 

  52. 52. Deng, H. W., Chen, W. M., Recker, R. R. (2000) QTL fine mapping by measuring and testing for Hardy-Weinberg and linkage disequilibrium at a series of linked marker loci in extreme samples of populations. Am J Hum Genet 66, 1027–1045.

    Article  CAS  PubMed  Google Scholar 

  53. 53. Deng, H. W., Shen, H., Xu, F. H., et al. (2002) Tests of linkage and/or association of genes for vitamin D receptor, osteocalcin, and parathyroid hormone with bone mineral density. J Bone Miner Res 17, 678–686.

    Article  CAS  PubMed  Google Scholar 

  54. 54. Lander, E. S., Schork, N. J. (1994) Genetic dissection of complex traits. Science 265,2037–2048.

    Article  CAS  PubMed  Google Scholar 

  55. 55. Allison, D. B. (1997) Transmission-disequilibrium tests for quantitative traits. Am J Hum Genet 60, 676–690.

    CAS  PubMed  Google Scholar 

  56. 56. Risch, N., Merikangas, K. (1996) The future of genetic studies of complex human diseases.Science 273, 1516–1517.

    Article  CAS  PubMed  Google Scholar 

  57. 57. Xiong, M. M., Krushkal, J., Boerwinkle, E. (1998) TDT statistics for mapping quantitative trait loci. Ann Hum Genet 62, 431–452.

    Article  CAS  PubMed  Google Scholar 

  58. 58. Abecasis, G. R., Noguchi, E., Heinzmann, A., et al. (2001) Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Genet 68, 191–197.

    Article  CAS  PubMed  Google Scholar 

  59. 59. Mangin, B., Thoquet, P., Olivier, J., et al. (1999) Temporal and multiple quantitative trait loci analyses of resistance to bacterial wilt in tomato permit the resolution of linked loci. Genetics 151, 1165–1172.

    CAS  PubMed  Google Scholar 

  60. 60. Weller, J. I., Song, J. Z., Heyen, D. W., et al. (1998) A new approach to the problem of multiple comparisons in the genetic dissection of complex traits. Genetics 150, 1699–1706.

    CAS  PubMed  Google Scholar 

  61. 61. Eaves, L. J. (1994) Effect of genetic architecture on the power of human linkage studies to resolve the contribution of quantitative trait loci. Heredity 72, 175–192.

    Article  PubMed  Google Scholar 

  62. 62. Mitchell, B. D., Ghosh, S., Schneider, J. L., et al. (1997) Power of variance component linkage analysis to detect epistasis. Genet Epidemiol 14, 1017–1022.

    Article  CAS  PubMed  Google Scholar 

  63. 63. Moore, J. H., Williams, S. M. (2002) New strategies for identifying gene-gene interactions in hypertension. Ann Med 34, 88–95.

    Article  CAS  PubMed  Google Scholar 

  64. 64. Storey, J. D., Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440–9445.

    Article  CAS  PubMed  Google Scholar 

  65. 65. Hao, K., Li, C., Rosenow, C., et al. (2004) Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10 K array. Eur J Hum Genet 12, 1001–1006.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Investigators of this work were partially supported by grants from NIH (R01 AR050496, K01 AR02170-01, R01 AR45349-01, and R01 GM60402-01A1) and an LB595 grant from the state of Nebraska. The study also benefited from grants from National Science Foundation of China, Huo Ying Dong Education Foundation, HuNan Province, Xi'an Jiaotong University, and the Ministry of Education of China.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Xiong, DH. et al. (2008). Quantitative Trait Loci Mapping. In: Westendorf, J.J. (eds) Osteoporosis. Methods In Molecular Biology™, vol 455. Humana Press. https://doi.org/10.1007/978-1-59745-104-8_16

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-104-8_16

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-828-7

  • Online ISBN: 978-1-59745-104-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics