Mixed model analysis of quantitative trait loci - PubMed (original) (raw)

Mixed model analysis of quantitative trait loci

S Xu et al. Proc Natl Acad Sci U S A. 2000.

Abstract

We develop a mixed model approach of quantitative trait locus (QTL) mapping for a hybrid population derived from the crosses of two or more distinguished outbred populations. Under the mixed model, we treat the mean allelic value of each source population as the fixed effect and the allelic deviations from the mean as random effects so that we can partition the total genetic variance into between- and within-population variances. Statistical inference of the QTL parameters is obtained by using the Bayesian method implemented by Markov chain Monte Carlo (MCMC). This unified QTL mapping algorithm treats the fixed and random model approaches as special cases of the general mixed model methodology. Utility and flexibility of the method are demonstrated by using a set of simulated data.

PubMed Disclaimer

Figures

Figure 1

QTL intensity profiles (a and b) and profiles of the effects (c and d) for the mixed model analysis. Markers (codominant) are evenly distributed with 10 cM apart. (a and c) Chromosome I. (b and_d_) Chromosome II. The true positions of the three QTL are pointed to by the arrows on the horizontal axes. The solid, dashed, and dotted lines represent for the population difference b =_b_2 − _b_1, variance within population one σ12, and variance within population two σ22, respectively.

Figure 2

Weighted QTL intensity profiles for the mixed model analysis. (a) Chromosome I. (b) Chromosome II.

Figure 3

QTL intensity profiles (a and b) and effect profiles (c and d) for the fixed model analysis. (a and c) Chromosome I. (b and_d_) Chromosome II.

Figure 4

Weighted QTL intensity profiles for the fixed model analysis. (a) Chromosome I. (b) Chromosome II.

Similar articles

• A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci.
  Yi N. Yi N. Genetics. 2004 Jun;167(2):967-75. doi: 10.1534/genetics.104.026286. Genetics. 2004. PMID: 15238545 Free PMC article.
• Markov chain Monte Carlo for mapping a quantitative trait locus in outbred populations.
  Bink MC, Janss LL, Quaas RL. Bink MC, et al. Genet Res. 2000 Apr;75(2):231-41. doi: 10.1017/s0016672399004310. Genet Res. 2000. PMID: 10816980
• Bayesian mapping of quantitative trait loci under complicated mating designs.
  Yi N, Xu S. Yi N, et al. Genetics. 2001 Apr;157(4):1759-71. doi: 10.1093/genetics/157.4.1759. Genetics. 2001. PMID: 11290729 Free PMC article.
• QTL analysis in arbitrary pedigrees with incomplete marker information.
  Vogl C, Xu S. Vogl C, et al. Heredity (Edinb). 2002 Nov;89(5):339-45. doi: 10.1038/sj.hdy.6800136. Heredity (Edinb). 2002. PMID: 12399991 Review.
• Bayesian Inference for Mixed Model-Based Genome-Wide Analysis of Expression Quantitative Trait Loci by Gibbs Sampling.
  Lee C. Lee C. Front Genet. 2019 Mar 22;10:199. doi: 10.3389/fgene.2019.00199. eCollection 2019. Front Genet. 2019. PMID: 30967893 Free PMC article. Review.

Cited by

• Association analysis for udder health based on SNP-panel and sequence data in Danish Holsteins.
  Wu X, Lund MS, Sahana G, Guldbrandtsen B, Sun D, Zhang Q, Su G. Wu X, et al. Genet Sel Evol. 2015 Jun 19;47(1):50. doi: 10.1186/s12711-015-0129-1. Genet Sel Evol. 2015. PMID: 26087655 Free PMC article.
• Generalized linear mixed models for mapping multiple quantitative trait loci.
  Che X, Xu S. Che X, et al. Heredity (Edinb). 2012 Jul;109(1):41-9. doi: 10.1038/hdy.2012.10. Epub 2012 Mar 14. Heredity (Edinb). 2012. PMID: 22415425 Free PMC article.
• Overview of QTL detection in plants and tests for synergistic epistatic interactions.
  Jannink JL, Moreau L, Charmet G, Charcosset A. Jannink JL, et al. Genetica. 2009 Jun;136(2):225-36. doi: 10.1007/s10709-008-9306-2. Epub 2008 Aug 10. Genetica. 2009. PMID: 18695990
• A comparison of founder-only and all-pedigree-members genotype-expression association by regression analysis.
  Suh YJ, Lee HS, Batliwalla F, Li W. Suh YJ, et al. BMC Proc. 2007;1 Suppl 1(Suppl 1):S8. doi: 10.1186/1753-6561-1-s1-s8. Epub 2007 Dec 18. BMC Proc. 2007. PMID: 18466582 Free PMC article.
• Bayesian shrinkage analysis of quantitative trait Loci for dynamic traits.
  Yang R, Xu S. Yang R, et al. Genetics. 2007 Jun;176(2):1169-85. doi: 10.1534/genetics.106.064279. Epub 2007 Apr 15. Genetics. 2007. PMID: 17435239 Free PMC article.

References

1. 1. Lander E S, Botstein D. Genetics. 1989;121:185–199. - PMC - PubMed
2. 1. Haley C S, Knott S A, Elsen J-M. Genetics. 1994;136:1195–1207. - PMC - PubMed
3. 1. Fernando R L, Grossman M. Genet Sel Evol. 1989;21:467–477.
4. 1. Sobel E, Lange K. Am J Hum Genet. 1996;58:1323–1337. - PMC - PubMed
5. 1. Wang C S, Rutledge J J, Gianola D. Genet Sel Evol. 1993;25:41–62.

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Atypon
  • Europe PubMed Central
  • PubMed Central