Abstract
In crop species, most QTL (quantitative trait loci) mapping strategies use segregating populations derived from an initial cross between two lines. However, schemes including more than two parents could also be used. We propose an approach using a high-density restriction fragment length polymorphism (RFLP) map established on six F 2 populations derived from diallel crosses among four inbred lines and the phenotypic performances of two types of replicated progenies (F 3 and topcross). The QTL is supposed to be on the marker locus considered. Three linear model tests for the detection of QTL effects (T 1, T 2 and T 3) are described and their power studied for the two types of progeny. T 1 tests the global genetic effects of the QTL (additivity and dominance) and T 2 tests only additive effects assuming dominance is absent when it could exist. The models of these two tests assume that the main effects of QTL alleles are constant in different genetic backgrounds. The additive model of test T 3 considers the six F 2 populations independently, and T 3 is the equivalent of the classical mean comparison test if we neglect dominance; it uses only contrasts between the homozygote marker classes. The results show that T 2 is much more powerful than T 3. The power of T 1 and T 2 depends on the relative sizes of the additive and dominance effects, and their comparison is not easy to establish. Nevertheless, T 2 seems to be the more powerful in most situations, indicating that it is often more interesting to ignore dominance when testing for a QTL effect. For a given size of genetic effects, the power is affected by the total number of individuals genotyped in F 2 and the recombination rate between the marker locus and the putative QTL. The approach presented in this paper has some drawbacks but could be easily generalized to other sizes of diallels and different progeny types.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Beckmann JS, Soller M (1986) Restriction fragment length polymorphism in plant genetic improvement. In: Miflin BJ (ed) Oxford surveys of plant molecular and cell biology vol 3. Oxford Press, Oxford, pp 197–250
Beckmann JS, Soller M (1988) Detection of linkage between marker loci and loci affecting quantitative traits in crosses between segregating populations. Theor Appl Genet 76:228–236
Carbonell EA, Gerig TM, Balansard E, Asins MJ (1992). Interval mapping in the analysis of nonadditive quantitative trait loci. Biometrics 48:305–315
Cowen NM (1988) The use of replicated progenies in marker-based mapping of QTLs. Theor Appl Genet 75:857–862
Edwards MD, Stuber CW, Wendel JF (1987) Molecular-marker-facilitated investigation of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113–125
Edwards MD, Helentjaris T, Wright S, Stuber CW (1992) Molecular-markar-facilitated investigations of quantiative trait loci in maize. 4. Analysis based on genome saturation with isozyme and restriction fragment length polymorphism markers. Theor Appl Genet 83:765–774
Ellis THN (1986) Restriction fragment length polymorphism markers in relation to quantitative characters. Theor Appl Genet 72:1–2
Graybill FA (1976) Theory and application of the linear model. Wadsworth, Belmont, Calif.
Jayakar SD (1970) On the detection and estimation of linkage between a locus influencing a quantitative character and a marker locus. Biometrics 26:466–479
Knapp SJ, Bridges WC (1990) Using molecular markers to estimate quantitative trait locus parameters: power and genetic variances for unreplicated and replicated progeny. Genetics 126:769–777
Knapp SJ, Bridges WC, Brikes D (1990) Mapping quantitative trait loci using molecular marker linkage maps. Theor Appl Genet 79:583–592
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
Luo ZW, Kearsey MJ (1989) Maxiumum likelihood estimation of linkage between a marker gene and a quantitative trait locus. Heredity 63:401–408
Luo ZW, Kearsey MJ (1991) Maximum likelihood estimation of linkage between a marker gene and a quantitative trait locus. II. Application to backcross and doubled haploid populations. Heredity 66:117–124
Ooijen JW van (1992) Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803–811
Sax K (1923) The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgarus. Genetics 8:552–560
Simpson SP (1989) Detection of linkage between quantitative trait loci and restriction fragment length polymorphisms using inbred line. Theor Appl Genet 77:815–819
Smith OS, Smith JSC, Bowen SL, Tenborg RA, Wall SJ (1990) Similarities among a group of elite maize imbreds as measured by pedigree, F1 grain yield, grain yield, heterosis and RFLPs. Theor Appl Genet 80:833–840
Soller M, Beckmann JS (1990) marker-based mapping of quantitative trait loci using replicated progenies. Theor Appl Genet 80:205–208
Soller M, Genizi A (1978) The efficiency of experimental designs for the detection of linkage between a marker locus and a locus affecting a quantitative trait in segregating populations. Biometrics 34:47–55
Soller M, Genizi A, Brody T (1976) On the power of experimental designs for the detection of linkage between marker loci and quantiative loci in crosses between inbred lines. Theor Appl Genet 47:35–39
Stuber CW, Edwards MD, Wendel JF (1987) Molecular-marker-facilitated investigations of quantitative-trait loci in maize. II. Factors influencing yield and its component traits. Crop Sci 27:629–648
Tanksley SD, Medina-Filho H, Rick CM (1982) Use of naturally-occurring enzyme variation to detect and map genes controlling quantitative traits in an interspecific backcross of tomato. Heredity 49:11–25
Thompson JN, Thoday JM (1979) Quantitative genetic variation. Academic Press, London
Weller JI (1986) Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers. Biometrics 42:627–640
Weller JI, Soller M, Brody T (1988) Linkage analysis of quantitative traits in an interspecific cross of tomato (Lycopersicon esculentum x Lycopersicon pimpinellifolium) by means of genetic markers. Genetics 118:3229–339
Author information
Authors and Affiliations
Additional information
Communicated by A. R. Hallauer
Rights and permissions
About this article
Cite this article
Rebai, A., Goffinet, B. Power of tests for QTL detection using replicated progenies derived from a diallel cross. Theoret. Appl. Genetics 86, 1014–1022 (1993). https://doi.org/10.1007/BF00211055
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00211055