Abstract
Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two lines. The power of such QTL detection and mapping strategies and the estimation of the effects highly depend on the choice of the two parental lines. Thus, the QTL detected in such populations only represent a small part of the genetic architecture of the trait. Besides, the effects of only two alleles are characterized, which is of limited interest to the breeder. On the other hand, common pedigree breeding material remains unexploited for QTL mapping. From a pre-breeding perspective, the utilization of the good quality phenotypic data generated by breeders can be improved through the search and manipulation of QTL. The development of statistical techniques suitable for QTL mapping in general conventional breeding populations is thus challenging. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population coming from inbred parents. The proposed developments attempt to make full use of any inferable relatedness information between the parents. The power and accuracy of this method were assessed on simulated data mimicking conventional breeding programs in cereals, in an effort to reproduce actual conditions of marker and gene allelic frequencies across the parental lines. A wide range of breeding scenarios and of genetic architectures was explored. We demonstrated that taking into account the estimable relatedness between the parents significantly improved the power and accuracy of the QTL parameter estimations.
Similar content being viewed by others
References
Bernardo, R., 1993. Estimation of coefficient of coancestry using molecular markers in maize. Theor Appl Genet 85: 1055–1062.
Dempster, A.P., N.M. Laird & D.B. Rubin, 1977. Maximum likelihood from incomplete data via the EM algorithm. J Royal Stat Soc 39: 1–38.
George A.W., P.M. Visscher & C.S. Haley, 2000. Mapping quantita-tive trait in complex pedigrees: A two-step variance component approach. Genetics 156: 2081–2092.
Gilmour, A.R., B.R. Cullis, S.J. Welham & R. Thompson, 1998. ASREML. Program User Manual. Orange Agricultural Institute, New South Wales, Australia.
Gimelfarb, A. & R. Lande, 1994. Simulation of marker-assisted se-lection in hybrid populations. Genet Res 63: 39–47.
Gimelfarb, A. & R. Lande, 1995. Marker-assisted selection and marker–QTL associations in hybrid populations. Theor Appl Genet 91: 522–528.
Hospital, F., L. Moreau, F. Lacoudre, A. Charcosset & A. Gallais, 1997. More on the efficiency of marker-assisted selection. Theor Appl Genet 95: 1181–1189.
Moreau, L., A. Charcosset, F. Hospital & A. Gallais, 1998. Marker-assisted selection efficiency in populations of finite size. Genetics 148: 1353–1365.
Servin, B., C. Dillmann, G. Decoux & F. Hospital, 2002. MDM: A program to compute fully informative genotype frequencies in complex breeding schemes. J Hered 93(3): 227–228.
Xie, C., D.D.G. Gessler & S. Xu, 1998. Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method. Genetics 149: 1139–1146.
Xu, S. 1998. Mapping quantitative trait loci using multiple families of line crosses. Genetics 148: 517–524.
Yi, N.& S. Xu, 2001. Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics 157: 1759–1771.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Crepieux, S., Lebreton, C., Servin, B. et al. IBD-based QTL detection in inbred pedigrees: A case study of cereal breeding programs. Euphytica 137, 101–109 (2004). https://doi.org/10.1023/B:EUPH.0000040507.44711.93
Issue Date:
DOI: https://doi.org/10.1023/B:EUPH.0000040507.44711.93