• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Dec 2000; 156(4): 2081–2092.
PMCID: PMC1461399

Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach.


There is a growing need for the development of statistical techniques capable of mapping quantitative trait loci (QTL) in general outbred animal populations. Presently used variance component methods, which correctly account for the complex relationships that may exist between individuals, are challenged by the difficulties incurred through unknown marker genotypes, inbred individuals, partially or unknown marker phases, and multigenerational data. In this article, a two-step variance component approach that enables practitioners to routinely map QTL in populations with the aforementioned difficulties is explored. The performance of the QTL mapping methodology is assessed via its application to simulated data. The capacity of the technique to accurately estimate parameters is examined for a range of scenarios.

Full Text

The Full Text of this article is available as a PDF (318K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Almasy L, Blangero J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet. 1998 May;62(5):1198–1211. [PMC free article] [PubMed]
  • Amos CI. Robust variance-components approach for assessing genetic linkage in pedigrees. Am J Hum Genet. 1994 Mar;54(3):535–543. [PMC free article] [PubMed]
  • Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. [PMC free article] [PubMed]
  • Elston RC, Stewart J. A general model for the genetic analysis of pedigree data. Hum Hered. 1971;21(6):523–542. [PubMed]
  • Lin S, Thompson E, Wijsman E. Achieving irreducibility of the Markov chain Monte Carlo method applied to pedigree data. IMA J Math Appl Med Biol. 1993;10(1):1–17. [PubMed]
  • Fulker DW, Cherny SS, Cardon LR. Multipoint interval mapping of quantitative trait loci, using sib pairs. Am J Hum Genet. 1995 May;56(5):1224–1233. [PMC free article] [PubMed]
  • Lin S, Thompson E, Wijsman E. Finding noncommunicating sets for Markov chain Monte Carlo estimations on pedigrees. Am J Hum Genet. 1994 Apr;54(4):695–704. [PMC free article] [PubMed]
  • George AW, Mengersen KL, Davis GP. Localization of a quantitative trait locus via a Bayesian approach. Biometrics. 2000 Mar;56(1):40–51. [PubMed]
  • Stram DO, Lee JW. Variance components testing in the longitudinal mixed effects model. Biometrics. 1994 Dec;50(4):1171–1177. [PubMed]
  • Heath SC. Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. Am J Hum Genet. 1997 Sep;61(3):748–760. [PMC free article] [PubMed]
  • Uimari P, Hoeschele I. Mapping-linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. Genetics. 1997 Jun;146(2):735–743. [PMC free article] [PubMed]
  • Van Arendonk JA, Tier B, Kinghorn BP. Use of multiple genetic markers in prediction of breeding values. Genetics. 1994 May;137(1):319–329. [PMC free article] [PubMed]
  • Hoeschele I, Uimari P, Grignola FE, Zhang Q, Gage KM. Advances in statistical methods to map quantitative trait loci in outbred populations. Genetics. 1997 Nov;147(3):1445–1457. [PMC free article] [PubMed]
  • Visscher PM, Haley CS, Heath SC, Muir WJ, Blackwood DH. Detecting QTLs for uni- and bipolar disorder using a variance component method. Psychiatr Genet. 1999 Jun;9(2):75–84. [PubMed]
  • Jansen RC, Johnson DL, Van Arendonk JA. A mixture model approach to the mapping of quantitative trait loci in complex populations with an application to multiple cattle families. Genetics. 1998 Jan;148(1):391–399. [PMC free article] [PubMed]
  • Jayakar SD. On the detection and estimation of linkage between a locus influencing a quantitative character and a marker locus. Biometrics. 1970 Sep;26(3):451–464. [PubMed]
  • Xie C, Gessler DD, Xu S. Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method. Genetics. 1998 Jun;149(2):1139–1146. [PMC free article] [PubMed]
  • Xu S, Atchley WR. A random model approach to interval mapping of quantitative trait loci. Genetics. 1995 Nov;141(3):1189–1197. [PMC free article] [PubMed]
  • Lander E, Kruglyak L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet. 1995 Nov;11(3):241–247. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...