Association of Marker Loci and QTL from Crosses of Inbred Parental Lines

  • Lee, Gi-Woong (Division of Animal Genomics and Bioinformatics, National Livestock Research Institute)
  • Received : 2004.07.12
  • Accepted : 2005.01.20
  • Published : 2005.06.01


The objectives of this study were to examine problems with using F$_1$ data by simulation, association of marker loci and QTL from crosses of inbred parental lines and to enumerate the preliminary characterization of genetic superiority within inbred parental lines. In this study, the association between markers for QTL used as covariates and estimates of variance components due to effects of lines was investigated through computer simulation. The effects of size of population to develop inbred lines and initial frequencies and magnitudes of effects of QTL were also considered. Results show that estimates of variance components due to line effects are influenced by including marker information as covariates in the model for analysis. Estimates of line variance were increased by adding marker information into the analysis, because negative covariances between effects associated with the markers and the remaining effects associated with other loci existed. However, the fit of the model as indicated by the log likelihood improved by adding more markers as covariates into the analysis. Marker assisted selection will be beneficial when markers explain unexplained genetic difference during selection procedure. Markers can be used to identify QTLs affecting traits, and to select for favorable QTL alleles. To efficiently use genetic markers, location of markers at the genome must be identified. The estimates of variance due to effects of with and without marker information used as covariates in the analysis were investigated. The estimates of line variances were always increased when markers were included as covariates for the model because a negative covariance were existed.


  1. Beckmann, J. S. and M. Soller. 1983. Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs. Theor. Appl. Genet. 67:35-43.
  2. Boldman, K. G., L. A. Kriese, L. D. Van Vleck, C. P. Van Tassell and S. D. Kachman. 1995. A manual for use of MTDFREML. A set of programs to obtain estimates of variances and covariances. U.S. Department of Agriculture, Agricultural Research Service. Clay Center, NE.
  3. Edwards, M. D., C. W. Stuber and J. F. Wendel. 1987. Molecularmarker-facilitated investigations of quantitative trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113-125.
  4. Jansen, R. C. 1994. Controlling the type I and type II errors in mapping quantitative trait loci. Genetics 138:871-881.
  5. Kashi, Y., F. Iraqi, Y. Tikochisky, B. Ruzitsky, A. Nave, J. S. Beckmann, A. Friedmann, M. Soller and Y. Gruenbaum. 1990. (TG)n uncovers a sex-specific hybridization pattern in cattle. Genomics 7:31-36.
  6. Soller, M. and J. S. Beckmann. 1983. Genetic polymorphism in varietal identification and genetic improvement. Theor. Appl. Genet. 67:25-33.
  7. Spelman, R. and D. Garrick. 1997. Utilisation of marker assisted selection in a commercial dairy cow population. Lives. Prod. Sci. 47:139-147.
  8. Stuber, C. W., M. D. Edwards and J. F. Wendel. 1987. Molecular marker-facilitated investigations of quantitative trait loci. II. Factors influencing yield and its component traits. Crop. Sci. 27:639-648.
  9. Van Zyl, C. M. 1998. Estimation of genetic parameters for production traits of corn and dual purpose sheep. Ph. D. thesis. Department of Animal Science. University of Nebraska-Lincoln, Lincoln, Nebraska.
  10. Weller, J. I. 1987. Mapping and analysis of quantitative trait loci in Lycopersicon. Heredity 59:413-421.
  11. Weller, J. I., M. Soller and T. Brody. 1988. Linkage analysis of quantitative traits in an interspecific cross of tomato (Lycopersicon esculentum${\times}$Lycopersicon pimpinellifolium) by means of genetic markers. Genetics 118:329-339.
  12. Zhuchenko, A. A., A. P. Samovol, A. B. Korol and V. K. Andryushchenko. 1979. Linkage between loci of quantitative characters and marker loci. II Influence of three tomoto chromosomes on variability of five quantitative characters in backcross progenies. Genetika 15:672-683.