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Theor Appl Genet. 2007 Dec;116(1):95-111. Epub 2007 Oct 20.

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

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School of Agriculture, Food and Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, Australia.


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.

[Indexed for MEDLINE]

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