A simple regression method for mapping quantitative trait loci in line crosses using flanking markers

@article{Haley1992ASR,
  title={A simple regression method for mapping quantitative trait loci in line crosses using flanking markers},
  author={Chris S. Haley and Sara A. Knott},
  journal={Heredity},
  year={1992},
  volume={69},
  pages={315-324}
}
The use of flanking marker methods has proved to be a powerful tool for the mapping of quantitative trait loci (QTL) in the segregating generations derived from crosses between inbred lines. Methods to analyse these data, based on maximum-likelihood, have been developed and provide good estimates of QTL effects in some situations. Maximum-likelihood methods are, however, relatively complex and can be computationally slow. In this paper we develop methods for mapping QTL based on multiple… 
Aspects of maximum likelihood methods for the mapping of quantitative trait loci in line crosses
TLDR
The use of adjacent (flanking) marker pairs gave improved power for the detection of QTL over the use of single markers when markers were widely spaced and the QTL effect large and made the method less sensitive to violations of assumptions, for example non-normality of the distribution.
Methods for multiple-marker mapping of quantitative trait loci in half-sib populations
TLDR
The least-squares approach using multiple markers provides a fast method that can easily be extended to include additional effects, and a number of assumptions have been made in order to make the likelihood calculations feasible, however, and computationally it is still more demanding than the least-Squares approach.
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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.
Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method.
TLDR
This work adopts the identical by descent (IBD)-based variance component method originally applied to human linkage analysis by combining multiple line crosses as independent families and explores the properties of consensus QTL mapping and demonstrates the method with F2, backcross (BC), and full-sib (FS) families.
Combining Data From Multiple Inbred Line Crosses Improves the Power and Resolution of Quantitative Trait Loci Mapping
TLDR
It is demonstrated that the combined-cross analysis can improve the power to detect weak QTL, can narrow support intervals for QTL regions, and can be used to separate multiple QTL that colocalize by chance.
Mapping quantitative trait loci in crosses between outbred lines using least squares.
The use of genetic maps based upon molecular markers has allowed the dissection of some of the factors underlying quantitative variation in crosses between inbred lines. For many species crossing
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TLDR
A method to locate quantitative trait loci on a chromosome and to estimate their additive and dominance effects is described, and the estimates of location and gene effects are consistent and as reliable as conventional flanking-marker methods.
Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data.
TLDR
Two new probabilistic measures will be used to summarize the results from the statistical analysis: the (posterior) QTL intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and the locationwise distributions of the phenotypic effects of theQTLs.
Multiple regression approach to mapping of quantitative trait loci (QTL) based on sib-pair data: A theoretical analysis
The interval mapping method has been shown to be a powerful tool for mapping QTL. However, it is still a challenge to perform a simultaneous analysis of several linked QTLs, and to isolate multiple
Using the mixed model for interval mapping of quantitative trait loci in outbred line crosses.
TLDR
The animal model using parental observations is shown to have advantages in estimating QTL position and additive genotypic value, especially when the polygenic heritability is large and the number of progeny per parent is small.
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References

SHOWING 1-10 OF 18 REFERENCES
Aspects of maximum likelihood methods for the mapping of quantitative trait loci in line crosses
TLDR
The use of adjacent (flanking) marker pairs gave improved power for the detection of QTL over the use of single markers when markers were widely spaced and the QTL effect large and made the method less sensitive to violations of assumptions, for example non-normality of the distribution.
Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.
TLDR
A set of analytical methods that modify and extend the classical theory for mapping quantitative trait loci (QTLs) and allow a substantial reduction in the number of progeny that need to be scored with the DNA markers.
Mapping and analysis of quantitative trait loci in Lycopersicon (tomato) with the aid of genetic markers using approximate maximum likelihood methods
TLDR
Results support those presented previously based on simulated results and a positive control indicating that, for samples of this size, accurate estimates are derived by the maximum likelihood technique.
Use of DNA fingerprints for the detection of major genes for quantitative traits in domestic species.
The detection of marker loci linked to major genes or quantitative trait loci (QTL) of large effect in farm animal populations is of great potential value, both because it allows the easy
Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments.
TLDR
The results suggested that, for a trait with low heritability (soluble solids), the phenotype of F3 progeny could be predicted more accurately from the genotype of the F2 parent at QTLs than from the phenotypic variation of theF2 individual.
Biometrical genetics
TLDR
The authors claim that their extensions of the approach to cover the analysis and interpretation of maternal inheritance and sex-linkage in randomly mating populations, both natural and experimental, and to deal with populations of haploid organisms is vindication of their view.
Generalized Linear Models
The technique of iterative weighted linear regression can be used to obtain maximum likelihood estimates of the parameters with observations distributed according to some exponential family and
Statistical Modelling in GLIM.
TLDR
This chapter discusses the development of GLIM directives system defined structures in GLIM datasets and macros, and the use of regression models for calibration fatorial designs midding data.
Genstat 5 Reference Manual
Part 1 Introduction, terminology and syntax: Genstat programs characters items lists expressions and formulae statements how to compact programs conventions for examples in later chapters. Part 2 The
Recovery of inter-block information when block sizes are unequal
SUMMARY A method is proposed for estimating intra-block and inter-block weights in the analysis of incomplete block designs with block sizes not necessarily equal. The method consists of maximizing
...
1
2
...