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Open Access Open Badges Research article

Multiple-trait quantitative trait locus mapping with incomplete phenotypic data

Zhigang Guo12 and James C Nelson1*

Author Affiliations

1 Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA 66506

2 Syngenta Seeds, Inc., Clinton, Illinois, 61727, USA

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BMC Genetics 2008, 9:82  doi:10.1186/1471-2156-9-82

Published: 5 December 2008



Conventional multiple-trait quantitative trait locus (QTL) mapping methods must discard cases (individuals) with incomplete phenotypic data, thereby sacrificing other phenotypic and genotypic information contained in the discarded cases. Under standard assumptions about the missing-data mechanism, it is possible to exploit these cases.


We present an expectation-maximization (EM) algorithm, derived for recombinant inbred and F2 genetic models but extensible to any mating design, that supports conventional hypothesis tests for QTL main effect, pleiotropy, and QTL-by-environment interaction in multiple-trait analyses with missing phenotypic data. We evaluate its performance by simulations and illustrate with a real-data example.


The EM method affords improved QTL detection power and precision of QTL location and effect estimation in comparison with case deletion or imputation methods. It may be incorporated into any least-squares or likelihood-maximization QTL-mapping approach.