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QTL analysis: further uses of ‘marker regression’

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A variety of approaches are available for identifying the location and effect of QTL in segregating populations using molecular markers. However, these have problems in distinguishing two linked QTL, particularly in relation to the size of the test statistic when many independent tests are performed. An empirical method for obtaining the distribution of the test statistic for specific datasets is described, and its power for demonstrating the inadequacy of a single-QTL model is explored through computer simulation. The method is an extension of the previously described technique of ‘marker regression’, and it is applied here to demonstrate two situations in which it may be useful. Firstly, we examine the power of the technique to distinguish two, linked QTL from one and compare this ability with that of two contemporary methods, ‘Mapmaker/QTL’ and ‘regression mapping’. Secondly, we show how to combine information from two, or more, populations that may be segregating for different marker loci in a given linkage group. This is illustrated for two populations having in common just two linked marker loci although the sharing of loci is not a pre-requisite. Empirical tests are used to determine whether the same or different QTL are segregating and, if they are the same QTL, whether they are the same alleles. Evidence is discussed which suggests that the upper limit to the number of QTL that can be located for any single quantitative trait in a segregating populations is 12.

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  • Haldane IBS (1919) The combination of linkage values and the calculation of distances between the loci of linked factors. J Genet 8:299–309

    Google Scholar 

  • Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324

    Google Scholar 

  • Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of Northern American barley germ plasm. Theor Appl Genet 87:392–401

    Google Scholar 

  • Hyne V, Kearsey MJ, Martinez O, Gang W, Snape JW (1994) A partial genome assay for quantitative trait loci in wheat (Triticum aestivum) using different analytical techniques. Theor Appl Genet 89:735–741

    CAS  Google Scholar 

  • Hyne V, Kearsey MJ, Pike DJ, Snape JW (1995) QTL analysis: unreliability and bias in estimation procedures. Plant Molec Biol (in press)

  • Kearsey MJ, Hyne V (1994) QTL analysis: A simple marker regression approach. Theor Appl Genet 89:698–702

    Google Scholar 

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    CAS  PubMed  Google Scholar 

  • Martinez O, Curnow RNC (1993) Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 85:480–488

    Google Scholar 

  • Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721–726

    Article  CAS  PubMed  Google Scholar 

  • van Ooijen JW (1992) Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803–811

    Google Scholar 

  • Whitehead Institute (1993) Mapping genes controlling quantitative traits using Mapmaker/QTLversion 1.1: a tutorial and reference manual. Whitehead Institute, Cambridge, Mass

    Google Scholar 

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Communicated by G. Wenzel

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Hyne, V., Kearsey, M.J. QTL analysis: further uses of ‘marker regression’. Theoret. Appl. Genetics 91, 471–476 (1995).

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