Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. 2003 Feb; 163(2): 789–801.
PMCID: PMC1462468

Estimating polygenic effects using markers of the entire genome.


Molecular markers have been used to map quantitative trait loci. However, they are rarely used to evaluate effects of chromosome segments of the entire genome. The original interval-mapping approach and various modified versions of it may have limited use in evaluating the genetic effects of the entire genome because they require evaluation of multiple models and model selection. Here we present a Bayesian regression method to simultaneously estimate genetic effects associated with markers of the entire genome. With the Bayesian method, we were able to handle situations in which the number of effects is even larger than the number of observations. The key to the success is that we allow each marker effect to have its own variance parameter, which in turn has its own prior distribution so that the variance can be estimated from the data. Under this hierarchical model, we were able to handle a large number of markers and most of the markers may have negligible effects. As a result, it is possible to evaluate the distribution of the marker effects. Using data from the North American Barley Genome Mapping Project in double-haploid barley, we found that the distribution of gene effects follows closely an L-shaped Gamma distribution, which is in contrast to the bell-shaped Gamma distribution when the gene effects were estimated from interval mapping. In addition, we show that the Bayesian method serves as an alternative or even better QTL mapping method because it produces clearer signals for QTL. Similar results were found from simulated data sets of F(2) and backcross (BC) families.

Full Text

The Full Text of this article is available as a PDF (213K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ball RD. Bayesian methods for quantitative trait loci mapping based on model selection: approximate analysis using the Bayesian information criterion. Genetics. 2001 Nov;159(3):1351–1364. [PMC free article] [PubMed]
  • Bost B, Dillmann C, de Vienne D. Fluxes and metabolic pools as model traits for quantitative genetics. I. The L-shaped distribution of gene effects. Genetics. 1999 Dec;153(4):2001–2012. [PMC free article] [PubMed]
  • Bost B, de Vienne D, Hospital F, Moreau L, Dillmann C. Genetic and nongenetic bases for the L-shaped distribution of quantitative trait loci effects. Genetics. 2001 Apr;157(4):1773–1787. [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]
  • Edwards MD, Stuber CW, Wendel JF. Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics. 1987 May;116(1):113–125. [PMC free article] [PubMed]
  • Göring HH, Terwilliger JD, Blangero J. Large upward bias in estimation of locus-specific effects from genomewide scans. Am J Hum Genet. 2001 Dec;69(6):1357–1369. [PMC free article] [PubMed]
  • Hayes B, Goddard ME. The distribution of the effects of genes affecting quantitative traits in livestock. Genet Sel Evol. 2001 May-Jun;33(3):209–229. [PMC free article] [PubMed]
  • Jiang C, Zeng ZB. Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica. 1997;101(1):47–58. [PubMed]
  • Kao CH, Zeng ZB, Teasdale RD. Multiple interval mapping for quantitative trait loci. Genetics. 1999 Jul;152(3):1203–1216. [PMC free article] [PubMed]
  • Lander ES, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989 Jan;121(1):185–199. [PMC free article] [PubMed]
  • Sen S, Churchill GA. A statistical framework for quantitative trait mapping. Genetics. 2001 Sep;159(1):371–387. [PMC free article] [PubMed]
  • Sillanpä MJ, Arjas E. Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics. 1998 Mar;148(3):1373–1388. [PMC free article] [PubMed]
  • Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001 Apr;157(4):1819–1829. [PMC free article] [PubMed]
  • Whittaker JC, Thompson R, Denham MC. Marker-assisted selection using ridge regression. Genet Res. 2000 Apr;75(2):249–252. [PubMed]
  • Yi N, Xu S. Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics. 2001 Apr;157(4):1759–1771. [PMC free article] [PubMed]
  • Piepho HP. A quick method for computing approximate thresholds for quantitative trait loci detection. Genetics. 2001 Jan;157(1):425–432. [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]
  • 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]

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...