Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. 2004 May; 167(1): 485–498.
PMCID: PMC1470842

Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits.

Abstract

From simulation studies it is known that the allocation of experimental resources has a crucial effect on power of QTL detection as well as on accuracy and precision of QTL estimates. In this study, we used a very large experimental data set composed of 976 F(5) maize testcross progenies evaluated in 19 environments and cross-validation to assess the effect of sample size (N), number of test environments (E), and significance threshold on the number of detected QTL, the proportion of the genotypic variance explained by them, and the corresponding bias of estimates for grain yield, grain moisture, and plant height. In addition, we used computer simulations to compare the usefulness of two cross-validation schemes for obtaining unbiased estimates of QTL effects. The maximum, validated genotypic variance explained by QTL in this study was 52.3% for grain moisture despite the large number of detected QTL, thus confirming the infinitesimal model of quantitative genetics. In both simulated and experimental data, the effect of sample size on power of QTL detection as well as on accuracy and precision of QTL estimates was large. The number of detected QTL and the proportion of genotypic variance explained by QTL generally increased more with increasing N than with increasing E. The average bias of QTL estimates and its range were reduced by increasing N and E. Cross-validation performed well with respect to yielding asymptotically unbiased estimates of the genotypic variance explained by QTL. On the basis of our findings, recommendations for planning of QTL mapping experiments and allocation of experimental resources are given.

Full Text

The Full Text of this article is available as a PDF (241K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Allison David B, Fernandez Jose R, Heo Moonseong, Zhu Shankuan, Etzel Carol, Beasley T Mark, Amos Christopher I. Bias in estimates of quantitative-trait-locus effect in genome scans: demonstration of the phenomenon and a method-of-moments procedure for reducing bias. Am J Hum Genet. 2002 Mar;70(3):575–585. [PMC free article] [PubMed]
  • Bennewitz Jörn, Reinsch Norbert, Kalm Ernst. Improved confidence intervals in quantitative trait loci mapping by permutation bootstrapping. Genetics. 2002 Apr;160(4):1673–1686. [PMC free article] [PubMed]
  • Knapp SJ, Bridges WC. Using molecular markers to estimate quantitative trait locus parameters: power and genetic variances for unreplicated and replicated progeny. Genetics. 1990 Nov;126(3):769–777. [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]
  • Bouchez Agnès, Hospital Frédéric, Causse Mathilde, Gallais André, Charcosset Alain. Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines. Genetics. 2002 Dec;162(4):1945–1959. [PMC free article] [PubMed]
  • Lande R, Thompson R. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics. 1990 Mar;124(3):743–756. [PMC free article] [PubMed]
  • Doerge RW, Churchill GA. Permutation tests for multiple loci affecting a quantitative character. Genetics. 1996 Jan;142(1):285–294. [PMC free article] [PubMed]
  • Moreau L, Charcosset A, Hospital F, Gallais A. Marker-assisted selection efficiency in populations of finite size. Genetics. 1998 Mar;148(3):1353–1365. [PMC free article] [PubMed]
  • Fridman E, Pleban T, Zamir D. A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4718–4723. [PMC free article] [PubMed]
  • Frisch M, Bohn M, Melchinger AE. PLABSIM: software for simulation of marker-assisted backcrossing. J Hered. 2000 Jan-Feb;91(1):86–87. [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]
  • Haley CS, Knott SA. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb) 1992 Oct;69(4):315–324. [PubMed]
  • Utz HF, Melchinger AE, Schön CC. Bias and Sampling Error of the Estimated Proportion of Genotypic Variance Explained by Quantitative Trait Loci Determined From Experimental Data in Maize Using Cross Validation and Validation With Independent Samples. Genetics. 2000 Apr;154(3):1839–1849. [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]
  • 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

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

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

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...