Skip to main content
PMC home page
Genetics logoLink to Genetics
. 1999 Aug;152(4):1741–1752. doi: 10.1093/genetics/152.4.1741

Mapping quantitative trait loci by genotyping haploid tissues.

R L Wu 1
PMCID: PMC1460711  PMID: 10430598

Abstract

Mapping strategies based on a half- or full-sib family design have been developed to map quantitative trait loci (QTL) for outcrossing species. However, these strategies are dependent on controlled crosses where marker-allelic frequency and linkage disequilibrium between the marker and QTL may limit their application. In this article, a maximum-likelihood method is developed to map QTL segregating in an open-pollinated progeny population using dominant markers derived from haploid tissues from single meiotic events. Results from the haploid-based mapping strategy are not influenced by the allelic frequencies of markers and their linkage disequilibria with QTL, because the probabilities of QTL genotypes conditional on marker genotypes of haploid tissues are independent of these population parameters. Parameter estimation and hypothesis testing are implemented via expectation/conditional maximization algorithm. Parameters estimated include the additive effect, the dominant effect, the population mean, the chromosomal location of the QTL in the interval, and the residual variance within the QTL genotypes, plus two population parameters, outcrossing rate and QTL-allelic frequency. Simulation experiments show that the accuracy and power of parameter estimates are affected by the magnitude of QTL effects, heritability levels of a trait, and sample sizes used. The application and limitation of the method are discussed.

Full Text

The Full Text of this article is available as a PDF (155.9 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Dragani T. A., Zeng Z. B., Canzian F., Gariboldi M., Ghilarducci M. T., Manenti G., Pierotti M. A. Mapping of body weight loci on mouse chromosome X. Mamm Genome. 1995 Nov;6(11):778–781. doi: 10.1007/BF00539002. [DOI] [PubMed] [Google Scholar]
  2. Hoeschele I., Uimari P., Grignola F. E., Zhang Q., Gage K. M. Advances in statistical methods to map quantitative trait loci in outbred populations. Genetics. 1997 Nov;147(3):1445–1457. doi: 10.1093/genetics/147.3.1445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Jansen R. C., Johnson D. L., Van Arendonk J. A. 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. doi: 10.1093/genetics/148.1.391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Jansen R. C., Stam P. High resolution of quantitative traits into multiple loci via interval mapping. Genetics. 1994 Apr;136(4):1447–1455. doi: 10.1093/genetics/136.4.1447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kao C. H., Zeng Z. B. General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. Biometrics. 1997 Jun;53(2):653–665. [PubMed] [Google Scholar]
  6. Kao C. H., Zeng Z. B., Teasdale R. D. Multiple interval mapping for quantitative trait loci. Genetics. 1999 Jul;152(3):1203–1216. doi: 10.1093/genetics/152.3.1203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Knott S. A., Haley C. S. Maximum likelihood mapping of quantitative trait loci using full-sib families. Genetics. 1992 Dec;132(4):1211–1222. doi: 10.1093/genetics/132.4.1211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Lander E. S., Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989 Jan;121(1):185–199. doi: 10.1093/genetics/121.1.185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Liu J., Mercer J. M., Stam L. F., Gibson G. C., Zeng Z. B., Laurie C. C. Genetic analysis of a morphological shape difference in the male genitalia of Drosophila simulans and D. mauritiana. Genetics. 1996 Apr;142(4):1129–1145. doi: 10.1093/genetics/142.4.1129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Liu Z., Dekkers J. C. Least squares interval mapping of quantitative trait loci under the infinitesimal genetic model in outbred populations. Genetics. 1998 Jan;148(1):495–505. doi: 10.1093/genetics/148.1.495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Mackinnon M. J., Weller J. I. 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. doi: 10.1093/genetics/141.2.755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Nuzhdin S. V., Pasyukova E. G., Dilda C. L., Zeng Z. B., Mackay T. F. Sex-specific quantitative trait loci affecting longevity in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9734–9739. doi: 10.1073/pnas.94.18.9734. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Tulsieram L. K., Glaubitz J. C., Kiss G., Carlson J. E. Single tree genetic linkage mapping in conifers using haploid DNA from megagametophytes. Biotechnology (N Y) 1992 Jun;10(6):686–690. doi: 10.1038/nbt0692-686. [DOI] [PubMed] [Google Scholar]
  14. 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. doi: 10.1093/genetics/146.2.735. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Wilcox P. L., Amerson H. V., Kuhlman E. G., Liu B. H., O'Malley D. M., Sederoff R. R. Detection of a major gene for resistance to fusiform rust disease in loblolly pine by genomic mapping. Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):3859–3864. doi: 10.1073/pnas.93.9.3859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Xu S., Atchley W. R. A random model approach to interval mapping of quantitative trait loci. Genetics. 1995 Nov;141(3):1189–1197. doi: 10.1093/genetics/141.3.1189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Xu S. Mapping quantitative trait loci using multiple families of line crosses. Genetics. 1998 Jan;148(1):517–524. doi: 10.1093/genetics/148.1.517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Zeng Z. B. Precision mapping of quantitative trait loci. Genetics. 1994 Apr;136(4):1457–1468. doi: 10.1093/genetics/136.4.1457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Zeng Z. B. 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. doi: 10.1073/pnas.90.23.10972. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES