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Genetics. Nov 1995; 141(3): 1189–1197.
PMCID: PMC1206840

A Random Model Approach to Interval Mapping of Quantitative Trait Loci

Abstract

Mapping quantitative trait loci in outbred populations is important because many populations of organisms are noninbred. Unfortunately, information about the genetic architecture of the trait may not be available in outbred populations. Thus, the allelic effects of genes can not be estimated with ease. In addition, under linkage equilibrium, marker genotypes provide no information about the genotype of a QTL (our terminology for a single quantitative trait locus is QTL while multiple loci are referred to as QTLs). To circumvent this problem, an interval mapping procedure based on a random model approach is described. Under a random model, instead of estimating the effects, segregating variances of QTLs are estimated by a maximum likelihood method. Estimation of the variance component of a QTL depends on the proportion of genes identical-by-descent (IBD) shared by relatives at the locus, which is predicted by the IBD of two markers flanking the QTL. The marker IBD shared by two relatives are inferred from the observed marker genotypes. The procedure offers an advantage over the regression interval mapping in terms of high power and small estimation errors and provides flexibility for large sibships, irregular pedigree relationships and incorporation of common environmental and fixed effects.

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Selected References

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  • Amos CI, Elston RC. Robust methods for the detection of genetic linkage for quantitative data from pedigrees. Genet Epidemiol. 1989;6(2):349–360. [PubMed]
  • Churchill GA, Giovannoni JJ, Tanksley SD. Pooled-sampling makes high-resolution mapping practical with DNA markers. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):16–20. [PMC free article] [PubMed]
  • Amos CI, Elston RC, Wilson AF, Bailey-Wilson JE. A more powerful robust sib-pair test of linkage for quantitative traits. Genet Epidemiol. 1989;6(3):435–449. [PubMed]
  • Darvasi A, Soller M. Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics. 1994 Dec;138(4):1365–1373. [PMC free article] [PubMed]
  • Andersson L, Haley CS, Ellegren H, Knott SA, Johansson M, Andersson K, Andersson-Eklund L, Edfors-Lilja I, Fredholm M, Hansson I, et al. Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science. 1994 Mar 25;263(5154):1771–1774. [PubMed]
  • Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. [PMC free article] [PubMed]
  • Haldane JB, Waddington CH. Inbreeding and Linkage. Genetics. 1931 Jul;16(4):357–374. [PMC free article] [PubMed]
  • Fulker DW, Cardon LR. A sib-pair approach to interval mapping of quantitative trait loci. Am J Hum Genet. 1994 Jun;54(6):1092–1103. [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]
  • Goldgar DE. Multipoint analysis of human quantitative genetic variation. Am J Hum Genet. 1990 Dec;47(6):957–967. [PMC free article] [PubMed]
  • Goldgar DE, Oniki RS. Comparison of a multipoint identity-by-descent method with parametric multipoint linkage analysis for mapping quantitative traits. Am J Hum Genet. 1992 Mar;50(3):598–606. [PMC free article] [PubMed]
  • Jansen RC. Interval mapping of multiple quantitative trait loci. Genetics. 1993 Sep;135(1):205–211. [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]
  • 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]
  • Haley CS, Knott SA, Elsen JM. Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics. 1994 Mar;136(3):1195–1207. [PMC free article] [PubMed]
  • Khatib H, Darvasi A, Plotski Y, Soller M. Determining relative microsatellite allele frequencies in pooled DNA samples. PCR Methods Appl. 1994 Aug;4(1):13–18. [PubMed]
  • Haseman JK, Elston RC. The investigation of linkage between a quantitative trait and a marker locus. Behav Genet. 1972 Mar;2(1):3–19. [PubMed]
  • Jansen RC. Interval mapping of multiple quantitative trait loci. Genetics. 1993 Sep;135(1):205–211. [PMC free article] [PubMed]
  • Jansen RC. Controlling the type I and type II errors in mapping quantitative trait loci. Genetics. 1994 Nov;138(3):871–881. [PMC free article] [PubMed]
  • Knott SA, Haley CS. Maximum likelihood mapping of quantitative trait loci using full-sib families. Genetics. 1992 Dec;132(4):1211–1222. [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]
  • 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]
  • McMillan I, Robertson A. The power of methods for the detection of major genes affecting quantitative characters. Heredity (Edinb) 1974 Jun;32(3):349–356. [PubMed]
  • Olson JM, Wijsman EM. Linkage between quantitative trait and marker loci: methods using all relative pairs. Genet Epidemiol. 1993;10(2):87–102. [PubMed]
  • Pacek P, Sajantila A, Syvänen AC. Determination of allele frequencies at loci with length polymorphism by quantitative analysis of DNA amplified from pooled samples. PCR Methods Appl. 1993 May;2(4):313–317. [PubMed]
  • Schork NJ. Extended multipoint identity-by-descent analysis of human quantitative traits: efficiency, power, and modeling considerations. Am J Hum Genet. 1993 Dec;53(6):1306–1319. [PMC free article] [PubMed]
  • Van Arendonk JA, Tier B, Kinghorn BP. Use of multiple genetic markers in prediction of breeding values. Genetics. 1994 May;137(1):319–329. [PMC free article] [PubMed]
  • Sax K. The Association of Size Differences with Seed-Coat Pattern and Pigmentation in PHASEOLUS VULGARIS. Genetics. 1923 Nov;8(6):552–560. [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]
  • Thompson JN., Jr Quantitative variation and gene number. Nature. 1975 Dec 25;258(5537):665–668. [PubMed]
  • Weller JI. Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers. Biometrics. 1986 Sep;42(3):627–640. [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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