Quantitative Trait Locus Mapping Based on Resampling in a Vast Maize Testcross Experiment and Its Relevance to Quantitative Genetics for Complex Traits

@article{Schn2004QuantitativeTL,
  title={Quantitative Trait Locus Mapping Based on Resampling in a Vast Maize Testcross Experiment and Its Relevance to Quantitative Genetics for Complex Traits},
  author={Chris-Carolin Sch{\"o}n and H. Friedrich Utz and Susanne Groh and Bernd Truberg and Stephen J. Openshaw and Albrecht E. Melchinger},
  journal={Genetics},
  year={2004},
  volume={167},
  pages={485 - 498}
}
From simulation studies it is known that the allocation of experimental resources has a crucial effect on power of QTL detection as well as on accuracy and precision of QTL estimates. In this study, we used a very large experimental data set composed of 976 F5 maize testcross progenies evaluated in 19 environments and cross-validation to assess the effect of sample size (N), number of test environments (E), and significance threshold on the number of detected QTL, the proportion of the… 
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References

SHOWING 1-10 OF 62 REFERENCES
Bias and Sampling Error of the Estimated Proportion of Genotypic Variance Explained by Quantitative Trait Loci Determined From Experimental Data in Maize Using Cross Validation and Validation With Independent Samples.
TLDR
CV with data from three QTL studies reported in the literature yielded similar results as those obtained with maize testcrosses, and is recommended for obtaining asymptotically unbiased estimates of p and consequently a realistic assessment of the prospects of MAS.
High resolution of quantitative traits into multiple loci via interval mapping.
TLDR
The core of the method is the completion of any missing genotypic (QTL and marker) observations, which is embedded in a general and simple expectation maximization (EM) algorithm to obtain maximum likelihood estimates of the model parameters.
Using molecular markers to estimate quantitative trait locus parameters: power and genetic variances for unreplicated and replicated progeny.
TLDR
How power is affected by r, n, and other factors is described to describe how power for testing hypotheses about means of QTL genotypes is increased by increasing r and n.
A simple regression method for mapping quantitative trait loci in line crosses using flanking markers
TLDR
Methods for mapping QTL based on multiple regression which can be applied using any general statistical package are developed and it is shown that these regression methods produce very similar results to those obtained using maximum likelihood.
Permutation tests for multiple loci affecting a quantitative character.
TLDR
Two extensions of the permutation-based method for estimating empirical threshold values are presented, which yield critical values that can be used to construct tests for the presence of minor QTL effects while accounting for effects of known major QTL.
Marker-assisted selection efficiency in populations of finite size.
TLDR
The efficiency of marker-assisted selection based on an index incorporating both phenotypic and molecular information is evaluated with an analytical approach that takes into account the size of the experiment and may be a useful tool to optimize the experimental means for more complex genetic situations.
Precision mapping of quantitative trait loci.
  • Z. Zeng
  • Biology, Medicine
    Genetics
  • 1994
TLDR
A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression, an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval.
Efficiency of marker-assisted selection in the improvement of quantitative traits.
TLDR
This work derives selection indices that maximize the rate of improvement in quantitative characters under different schemes of MAS combining information on molecular genetic polymorphisms (marker loci) with data on phenotypic variation among individuals (and their relatives).
Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines.
TLDR
The marker-assisted introgression of favorable alleles at three quantitative trait loci (QTL) for earliness and grain yield among maize elite lines proved successful at the genotypic level, as analyzed by precision graphical genotypes, although no emphasis was put on the reduction of linkage drag around QTL.
Improved confidence intervals in quantitative trait loci mapping by permutation bootstrapping.
TLDR
Three modified methods are proposed to calculate nonparametric bootstrap confidence intervals for QTL locations, which compute noncentral confidence intervals and correct the bootstrap distribution of the QTL estimates for the impact of the markers.
...
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5
...