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Genetics. Jul 1995; 140(3): 1111–1127.
PMCID: PMC1206666

Multiple Trait Analysis of Genetic Mapping for Quantitative Trait Loci


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.

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Selected References

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  • Begun DJ, Aquadro CF. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature. 1992 Apr 9;356(6369):519–520. [PubMed]
  • Boe L. Mechanism for induction of adaptive mutations in Escherichia coli. Mol Microbiol. 1990 Apr;4(4):597–601. [PubMed]
  • Cairns J, Overbaugh J, Miller S. The origin of mutants. Nature. 1988 Sep 8;335(6186):142–145. [PubMed]
  • Foster PL. Population dynamics of a Lac- strain of Escherichia coli during selection for lactose utilization. Genetics. 1994 Oct;138(2):253–261. [PMC free article] [PubMed]
  • Foster PL, Cairns J. Mechanisms of directed mutation. Genetics. 1992 Aug;131(4):783–789. [PMC free article] [PubMed]
  • Foster PL, Trimarchi JM. Adaptive reversion of a frameshift mutation in Escherichia coli by simple base deletions in homopolymeric runs. Science. 1994 Jul 15;265(5170):407–409. [PMC free article] [PubMed]
  • Hall BG. 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. [PMC free article] [PubMed]
  • Hall BG. Selection-induced mutations occur in yeast. Proc Natl Acad Sci U S A. 1992 May 15;89(10):4300–4303. [PMC free article] [PubMed]
  • Harris RS, Longerich S, Rosenberg SM. Recombination in adaptive mutation. Science. 1994 Apr 8;264(5156):258–260. [PubMed]
  • Langley CH, 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. [PMC free article] [PubMed]
  • Lenski RE, Mittler JE. The directed mutation controversy and neo-Darwinism. Science. 1993 Jan 8;259(5092):188–194. [PubMed]
  • Lenski RE, Slatkin M, Ayala FJ. 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. [PMC free article] [PubMed]
  • Luria SE, Delbrück M. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 1943 Nov;28(6):491–511. [PMC free article] [PubMed]
  • Mittler JE, Lenski RE. New data on excisions of Mu from E. coli MCS2 cast doubt on directed mutation hypothesis. Nature. 1990 Mar 8;344(6262):173–175. [PubMed]
  • Rosenberg SM, Longerich S, Gee P, Harris RS. Adaptive mutation by deletions in small mononucleotide repeats. Science. 1994 Jul 15;265(5170):405–407. [PubMed]
  • Shapiro JA. Observations on the formation of clones containing araB-lacZ cistron fusions. Mol Gen Genet. 1984;194(1-2):79–90. [PubMed]
  • Steele DF, Jinks-Robertson S. An examination of adaptive reversion in Saccharomyces cerevisiae. Genetics. 1992 Sep;132(1):9–21. [PMC free article] [PubMed]
  • Thomas AW, Lewington J, Hope S, Topping AW, Weightman AJ, Slater JH. Environmentally directed mutations in the dehalogenase system of Pseudomonas putida strain PP3. Arch Microbiol. 1992;158(3):176–182. [PubMed]
  • Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. [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]
  • Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander ES, Tanksley SD. Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics. 1991 Jan;127(1):181–197. [PMC free article] [PubMed]
  • Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES. 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. [PMC free article] [PubMed]
  • Zeng ZB. 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. [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]
  • Zeng ZB. Precision mapping of quantitative trait loci. Genetics. 1994 Apr;136(4):1457–1468. [PMC free article] [PubMed]

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