Look before you leap: a new approach to mapping QTL

In this paper, we present an innovative and powerful approach for mapping quantitative trait loci (QTL) in experimental populations. This deviates from the traditional approach of (composite) interval mapping which uses a QTL profile to simultaneously determine the number and location of QTL. Instea...

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Bibliographic Details
Published in:Theoretical and applied genetics 2009-09, Vol.119 (5), p.899-911
Main Authors: Huang, B. Emma, George, Andrew W
Format: Article
Language:English
Subjects:
Agriculture
Biochemistry
Biological and medical sciences
Biomedical and Life Sciences
Biotechnology
Chromosome Mapping - methods
Chromosomes
Classical genetics, quantitative genetics, hybrids
Crosses, Genetic
Feature selection
Fundamental and applied biological sciences. Psychology
Genetic Linkage
Genetics of eukaryotes. Biological and molecular evolution
Genome, Plant - genetics
Life Sciences
Localization
Original Paper
Plant Biochemistry
Plant Breeding/Biotechnology
Plant Genetics and Genomics
Pteridophyta, spermatophyta
Quantitative Trait Loci - genetics
Triticum - genetics
Triticum aestivum
Vegetals
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Summary:In this paper, we present an innovative and powerful approach for mapping quantitative trait loci (QTL) in experimental populations. This deviates from the traditional approach of (composite) interval mapping which uses a QTL profile to simultaneously determine the number and location of QTL. Instead, we look before we leap by employing separate detection and localization stages. In the detection stage, we use an iterative variable selection process coupled with permutation to identify the number and synteny of QTL. In the localization stage, we position the detected QTL through a series of one-dimensional interval mapping scans. Results from a detailed simulation study and real analysis of wheat data are presented. We achieve impressive increases in the power of QTL detection compared to composite interval mapping. We also accurately estimate the size and position of QTL. An R library, DLMap, implements the methods described here and is freely available from CRAN (http://cran.r-project.org/).
ISSN:0040-5752
1432-2242
DOI:10.1007/s00122-009-1098-y