The analysis of QTL by simultaneous use of the full linkage map

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Verbyla, A. P., Cullis, B. R. and Thompson, R. 2008. The analysis of QTL by simultaneous use of the full linkage map. Theoretical and Applied Genetics. 116 (December), pp. 95-111.

AuthorsVerbyla, A. P., Cullis, B. R. and Thompson, R.

An extension of interval mapping is presented that incorporates all intervals on the linkage map simultaneously. The approach uses a working model in which the sizes of putative QTL for all intervals across the genome are random effects. An outlier detection method is used to screen for possible QTL. Selected QTL are subsequently fitted as fixed effects. This screening and selection approach is repeated until the variance component for QTL sizes is not statistically significant. A comprehensive simulation study is conducted in which map uncertainty is included. The proposed method is shown to be superior to composite interval mapping in terms of power of detection of QTL. There is an increase in the rate of false positive QTL detected when using the new approach, but this rate decreases as the population size increases. The new approach is much simpler computationally. The analysis of flour milling yield in a doubled haploid population illustrates the improved power of detection of QTL using the approach, and also shows how vital it is to allow for sources of non-genetic variation in the analysis.

Year of Publication2008
JournalTheoretical and Applied Genetics
Journal citation116 (December), pp. 95-111
Digital Object Identifier (DOI)doi:10.1007/s00122-007-0650-x
Open accessPublished as non-open access
Funder project or codeCentre for Mathematical and Computational Biology (MCB)
Research in statistics relevant to biological processes
Output statusPublished
Publication dates
Online20 Oct 2007
Publication process dates
Accepted17 Sep 2007
Copyright licensePublisher copyright

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