Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Nov 1997; 147(3): 1445–1457.
PMCID: PMC1208265

Advances in Statistical Methods to Map Quantitative Trait Loci in Outbred Populations


Statistical methods to map quantitative trait loci (QTL) in outbred populations are reviewed, extensions and applications to human and plant genetic data are indicated, and areas for further research are identified. Simple and computationally inexpensive methods include (multiple) linear regression of phenotype on marker genotypes and regression of squared phenotypic differences among relative pairs on estimated proportions of identity-by-descent at a locus. These methods are less suited for genetic parameter estimation in outbred populations but allow the determination of test statistic distributions via simulation or data permutation; however, further inferences including confidence intervals of QTL location require the use of Monte Carlo or bootstrap sampling techniques. A method which is intermediate in computational requirements is residual maximum likelihood (REML) with a covariance matrix of random QTL effects conditional on information from multiple linked markers. Testing for the number of QTLs on a chromosome is difficult in a classical framework. The computationally most demanding methods are maximum likelihood and Bayesian analysis, which take account of the distribution of multilocus marker-QTL genotypes on a pedigree and permit investigators to fit different models of variation at the QTL. The Bayesian analysis includes the number of QTLs on a chromosome as an unknown.

Full Text

The Full Text of this article is available as a PDF (1.4M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Amos CI, Elston RC. Robust methods for the detection of genetic linkage for quantitative data from pedigrees. Genet Epidemiol. 1989;6(2):349–360. [PubMed]
  • Amos CI, Elston RC, Wilson AF, Bailey-Wilson JE. A more powerful robust sib-pair test of linkage for quantitative traits. Genet Epidemiol. 1989;6(3):435–449. [PubMed]
  • Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. [PMC free article] [PubMed]
  • Haley CS, Knott SA, Elsen JM. Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics. 1994 Mar;136(3):1195–1207. [PMC free article] [PubMed]
  • Jansen RC, Stam P. High resolution of quantitative traits into multiple loci via interval mapping. Genetics. 1994 Apr;136(4):1447–1455. [PMC free article] [PubMed]
  • Knott SA, Haley CS. Maximum likelihood mapping of quantitative trait loci using full-sib families. Genetics. 1992 Dec;132(4):1211–1222. [PMC free article] [PubMed]
  • Knott SA, Haley CS, Thompson R. Methods of segregation analysis for animal breeding data: a comparison of power. Heredity (Edinb) 1992 Apr;68(Pt 4):299–311. [PubMed]
  • Knott SA, Haley CS, Thompson R. Methods of segregation analysis for animal breeding data: parameter estimates. Heredity (Edinb) 1992 Apr;68(Pt 4):313–320. [PubMed]
  • Lin S. A scheme for constructing an irreducible Markov chain for pedigree data. Biometrics. 1995 Mar;51(1):318–322. [PubMed]
  • Lin S. Multipoint linkage analysis via Metropolis jumping kernels. Biometrics. 1996 Dec;52(4):1417–1427. [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]
  • 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]
  • Mackinnon MJ, Weller JI. Methodology and accuracy of estimation of quantitative trait loci parameters in a half-sib design using maximum likelihood. Genetics. 1995 Oct;141(2):755–770. [PMC free article] [PubMed]
  • Meuwissen TH, Goddard ME. Estimation of effects of quantitative trait loci in large complex pedigrees. Genetics. 1997 May;146(1):409–416. [PMC free article] [PubMed]
  • Olson JM, Wijsman EM. Linkage between quantitative trait and marker loci: methods using all relative pairs. Genet Epidemiol. 1993;10(2):87–102. [PubMed]
  • Satagopan JM, Yandell BS, Newton MA, Osborn TC. A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics. 1996 Oct;144(2):805–816. [PMC free article] [PubMed]
  • Sheehan N, Thomas A. On the irreducibility of a Markov chain defined on a space of genotype configurations by a sampling scheme. Biometrics. 1993 Mar;49(1):163–175. [PubMed]
  • Shrimpton AE, Robertson A. The Isolation of Polygenic Factors Controlling Bristle Score in Drosophila Melanogaster. II. Distribution of Third Chromosome Bristle Effects within Chromosome Sections. Genetics. 1988 Mar;118(3):445–459. [PMC free article] [PubMed]
  • Spelman RJ, Coppieters W, Karim L, van Arendonk JA, Bovenhuis H. Quantitative trait loci analysis for five milk production traits on chromosome six in the Dutch Holstein-Friesian population. Genetics. 1996 Dec;144(4):1799–1808. [PMC free article] [PubMed]
  • Stricker C, Fernando RL, Elston RC. Linkage analysis with an alternative formulation for the mixed model of inheritance: the finite polygenic mixed model. Genetics. 1995 Dec;141(4):1651–1656. [PMC free article] [PubMed]
  • Thomas DC, Cortessis V. A Gibbs sampling approach to linkage analysis. Hum Hered. 1992;42(1):63–76. [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]
  • Uimari P, Thaller G, Hoeschele I. The use of multiple markers in a Bayesian method for mapping quantitative trait loci. Genetics. 1996 Aug;143(4):1831–1842. [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]
  • Visscher PM, Thompson R, Haley CS. Confidence intervals in QTL mapping by bootstrapping. Genetics. 1996 Jun;143(2):1013–1020. [PMC free article] [PubMed]
  • Weller JI. Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers. Biometrics. 1986 Sep;42(3):627–640. [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]
  • Zeng ZB. Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):10972–10976. [PMC free article] [PubMed]
  • Zeng ZB. Precision mapping of quantitative trait loci. Genetics. 1994 Apr;136(4):1457–1468. [PMC free article] [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...


  • MedGen
    Related information in MedGen
  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...