Skip to main content
PMC home page
Genetics logoLink to Genetics
. 1995 Jul;140(3):1111–1127. doi: 10.1093/genetics/140.3.1111

Multiple Trait Analysis of Genetic Mapping for Quantitative Trait Loci

C Jiang 1, Z B Zeng 1
PMCID: PMC1206666  PMID: 7672582

Abstract

We present in this paper models and statistical methods for performing multiple trait analysis on mapping quantitative trait loci (QTL) based on the composite interval mapping method. By taking into account the correlated structure of multiple traits, this joint analysis has several advantages, compared with separate analyses, for mapping QTL, including the expected improvement on the statistical power of the test for QTL and on the precision of parameter estimation. Also this joint analysis provides formal procedures to test a number of biologically interesting hypotheses concerning the nature of genetic correlations between different traits. Among the testing procedures considered are those for joint mapping, pleiotropy, QTL by environment interaction, and pleiotropy vs. close linkage. The test of pleiotropy (one pleiotropic QTL at a genome position) vs. close linkage (multiple nearby nonpleiotropic QTL) can have important implications for our understanding of the nature of genetic correlations between different traits in certain regions of a genome and also for practical applications in animal and plant breeding because one of the major goals in breeding is to break unfavorable linkage. Results of extensive simulation studies are presented to illustrate various properties of the analyses.

Full Text

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

Selected References

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

  1. Begun D. J., Aquadro C. F. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature. 1992 Apr 9;356(6369):519–520. doi: 10.1038/356519a0. [DOI] [PubMed] [Google Scholar]
  2. Boe L. Mechanism for induction of adaptive mutations in Escherichia coli. Mol Microbiol. 1990 Apr;4(4):597–601. doi: 10.1111/j.1365-2958.1990.tb00628.x. [DOI] [PubMed] [Google Scholar]
  3. Cairns J., Overbaugh J., Miller S. The origin of mutants. Nature. 1988 Sep 8;335(6186):142–145. doi: 10.1038/335142a0. [DOI] [PubMed] [Google Scholar]
  4. Churchill G. A., Doerge R. W. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. doi: 10.1093/genetics/138.3.963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Foster P. L., Cairns J. Mechanisms of directed mutation. Genetics. 1992 Aug;131(4):783–789. doi: 10.1093/genetics/131.4.783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Foster P. L. Population dynamics of a Lac- strain of Escherichia coli during selection for lactose utilization. Genetics. 1994 Oct;138(2):253–261. doi: 10.1093/genetics/138.2.253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Foster P. L., Trimarchi J. M. Adaptive reversion of a frameshift mutation in Escherichia coli by simple base deletions in homopolymeric runs. Science. 1994 Jul 15;265(5170):407–409. doi: 10.1126/science.8023164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Haley C. S., Knott S. A. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb) 1992 Oct;69(4):315–324. doi: 10.1038/hdy.1992.131. [DOI] [PubMed] [Google Scholar]
  9. Hall B. G. Adaptive evolution that requires multiple spontaneous mutations: mutations involving base substitutions. Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5882–5886. doi: 10.1073/pnas.88.13.5882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hall B. G. Selection-induced mutations occur in yeast. Proc Natl Acad Sci U S A. 1992 May 15;89(10):4300–4303. doi: 10.1073/pnas.89.10.4300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Harris R. S., Longerich S., Rosenberg S. M. Recombination in adaptive mutation. Science. 1994 Apr 8;264(5156):258–260. doi: 10.1126/science.8146657. [DOI] [PubMed] [Google Scholar]
  12. Langley C. H., MacDonald J., Miyashita N., Aguadé M. Lack of correlation between interspecific divergence and intraspecific polymorphism at the suppressor of forked region in Drosophila melanogaster and Drosophila simulans. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1800–1803. doi: 10.1073/pnas.90.5.1800. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lenski R. E., Mittler J. E. The directed mutation controversy and neo-Darwinism. Science. 1993 Jan 8;259(5092):188–194. doi: 10.1126/science.7678468. [DOI] [PubMed] [Google Scholar]
  14. Lenski R. E., Slatkin M., Ayala F. J. Mutation and selection in bacterial populations: alternatives to the hypothesis of directed mutation. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2775–2778. doi: 10.1073/pnas.86.8.2775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Luria S. E., Delbrück M. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 1943 Nov;28(6):491–511. doi: 10.1093/genetics/28.6.491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Mittler J. E., Lenski R. E. New data on excisions of Mu from E. coli MCS2 cast doubt on directed mutation hypothesis. Nature. 1990 Mar 8;344(6262):173–175. doi: 10.1038/344173a0. [DOI] [PubMed] [Google Scholar]
  17. Paterson A. H., Damon S., Hewitt J. D., Zamir D., Rabinowitch H. D., Lincoln S. E., Lander E. S., Tanksley S. D. Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics. 1991 Jan;127(1):181–197. doi: 10.1093/genetics/127.1.181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rosenberg S. M., Longerich S., Gee P., Harris R. S. Adaptive mutation by deletions in small mononucleotide repeats. Science. 1994 Jul 15;265(5170):405–407. doi: 10.1126/science.8023163. [DOI] [PubMed] [Google Scholar]
  19. Shapiro J. A. Observations on the formation of clones containing araB-lacZ cistron fusions. Mol Gen Genet. 1984;194(1-2):79–90. doi: 10.1007/BF00383501. [DOI] [PubMed] [Google Scholar]
  20. Steele D. F., Jinks-Robertson S. An examination of adaptive reversion in Saccharomyces cerevisiae. Genetics. 1992 Sep;132(1):9–21. doi: 10.1093/genetics/132.1.9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Stuber C. W., Lincoln S. E., Wolff D. W., Helentjaris T., Lander E. S. Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics. 1992 Nov;132(3):823–839. doi: 10.1093/genetics/132.3.823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Thomas A. W., Lewington J., Hope S., Topping A. W., Weightman A. J., Slater J. H. Environmentally directed mutations in the dehalogenase system of Pseudomonas putida strain PP3. Arch Microbiol. 1992;158(3):176–182. doi: 10.1007/BF00290813. [DOI] [PubMed] [Google Scholar]
  23. Zeng Z. B. Correcting the bias of Wright's estimates of the number of genes affecting a quantitative character: a further improved method. Genetics. 1992 Aug;131(4):987–1001. doi: 10.1093/genetics/131.4.987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. 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]
  25. 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