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

Haley, C S; Knott, S A

doi:10.1038/hdy.1992.131

Cited by 1,991Genetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestockGenetic Associations and Epidemiology

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

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Haley, C S, Knott, S A·1992·Heredity

DOI 10.1038/hdy.1992.131

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Abstract

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 regression which can be applied using any general statistical package. We use the example of mapping in an F(2) population and show that these regression methods produce very similar results to those obtained using maximum likelihood. The relative simplicity of the regression methods means that models with more than a single QTL can be explored and we give examples of two lined loci and of two interacting loci. Other models, for example with more than two QTL, with environmental fixed effects, with between family variance or for threshold traits, could be fitted in a similar way. The ease, speed of application and generality of regression methods for flanking marker analysis, and the good estimates they obtain, suggest that they should provide the method of choice for the analysis of QTL mapping data from inbred line crosses.

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Within factorial regression models, markers can serve as explanatory variables, which is at the core of regression-based QTL mapping.
“For example, within the framework of factorial regression models, markers can serve as explanatory variables, which is at the core of regression–based approaches for QTL mapping (Haley and Knott, 1992; Martínez and Curnow, 1992).”
From The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis (2013) · cites this paper as Haley and Knott, 1992

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Self-citation

Authors: Haley, C. S., & Knott, S. A.
Affiliations: University of Edinburgh (GB)
ORCID: Haley, C S
Knott, S A
Venue: Heredity
Publisher: Springer Science and Business Media LLC
Published: 1992-10
Volume: 69
Issue: 4
Pages: 315-324
ISSN: 0018-067X (ISSN-L)
1365-2540
DOI: 10.1038/hdy.1992.131
OpenAlex: W2034608799
Cited by: 1,991
References: 19
Citations by year: 2026: 29 · 2025: 32 · 2024: 42 · 2023: 28 · 2022: 43 · 2021: 74 · 2020: 55 · 2019: 56 · 2018: 59 · 2017: 40 · 2016: 45 · 2015: 70 · 2014: 53 · 2013: 81 · 2012: 109
FWCI: 14.13
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springer.com/tdm (tdm)
Locations: Heredity (publishedVersion)
PubMed (publishedVersion)
Funders: Ministry of Agriculture, Forestry and Fisheries
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords: quantitative trait loci, QTL mapping, flanking markers, multiple linear regression, F2 population, maximum likelihood comparison, gene-gene interaction, threshold traits
MeSH terms: Animals, Chromosome Mapping, Computer Simulation, Crosses, Genetic, Genetic Markers, Inbreeding, Regression Analysis, Models, Statistical, Likelihood Functions, Quantitative Trait Loci

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

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