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Genetics. Jul 1999; 152(3): 1203–1216.
PMCID: PMC1460657

Multiple interval mapping for quantitative trait loci.


A new statistical method for mapping quantitative trait loci (QTL), called multiple interval mapping (MIM), is presented. It uses multiple marker intervals simultaneously to fit multiple putative QTL directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting genetic parameters and the method of maximum likelihood for estimating genetic parameters. With the MIM approach, the precision and power of QTL mapping could be improved. Also, epistasis between QTL, genotypic values of individuals, and heritabilities of quantitative traits can be readily estimated and analyzed. Using the MIM model, a stepwise selection procedure with likelihood ratio test statistic as a criterion is proposed to identify QTL. This MIM method was applied to a mapping data set of radiata pine on three traits: brown cone number, tree diameter, and branch quality scores. Based on the MIM result, seven, six, and five QTL were detected for the three traits, respectively. The detected QTL individually contributed from approximately 1 to 27% of the total genetic variation. Significant epistasis between four pairs of QTL in two traits was detected, and the four pairs of QTL contributed approximately 10.38 and 14.14% of the total genetic variation. The asymptotic variances of QTL positions and effects were also provided to construct the confidence intervals. The estimated heritabilities were 0.5606, 0.5226, and 0. 3630 for the three traits, respectively. With the estimated QTL effects and positions, the best strategy of marker-assisted selection for trait improvement for a specific purpose and requirement can be explored. The MIM FORTRAN program is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/).

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Selected References

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  • Hackett CA, Weller JI. Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics. 1995 Dec;51(4):1252–1263. [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]
  • 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]
  • Jayakar SD. On the detection and estimation of linkage between a locus influencing a quantitative character and a marker locus. Biometrics. 1970 Sep;26(3):451–464. [PubMed]
  • Jiang C, Zeng ZB. Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica. 1997;101(1):47–58. [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]
  • Li Z, Pinson SR, Park WD, Paterson AH, Stansel JW. Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics. 1997 Feb;145(2):453–465. [PMC free article] [PubMed]
  • Darvasi A, Weinreb A, Minke V, Weller JI, Soller M. Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics. 1993 Jul;134(3):943–951. [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]
  • Satagopan JM, Yandell BS, Newton MA, Osborn TC. A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics. 1996 Oct;144(2):805–816. [PMC free article] [PubMed]
  • Dupuis J, Siegmund D. Statistical methods for mapping quantitative trait loci from a dense set of markers. Genetics. 1999 Jan;151(1):373–386. [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]
  • Sillanpä MJ, Arjas E. Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics. 1998 Mar;148(3):1373–1388. [PMC free article] [PubMed]
  • Grattapaglia D, Sederoff R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics. 1994 Aug;137(4):1121–1137. [PMC free article] [PubMed]
  • Xu S, Atchley WR. A random model approach to interval mapping of quantitative trait loci. Genetics. 1995 Nov;141(3):1189–1197. [PMC free article] [PubMed]
  • Xu S, Atchley WR. Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics. 1996 Jul;143(3):1417–1424. [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]

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