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2014 ; 198
(1
): 129-37
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Multiple quantitative trait analysis using bayesian networks
#MMPMID25236454
Scutari M
; Howell P
; Balding DJ
; Mackay I
Genetics
2014[Sep]; 198
(1
): 129-37
PMID25236454
show ga
Models for genome-wide prediction and association studies usually target a single
phenotypic trait. However, in animal and plant genetics it is common to record
information on multiple phenotypes for each individual that will be genotyped.
Modeling traits individually disregards the fact that they are most likely
associated due to pleiotropy and shared biological basis, thus providing only a
partial, confounded view of genetic effects and phenotypic interactions. In this
article we use data from a Multiparent Advanced Generation Inter-Cross (MAGIC)
winter wheat population to explore Bayesian networks as a convenient and
interpretable framework for the simultaneous modeling of multiple quantitative
traits. We show that they are equivalent to multivariate genetic best linear
unbiased prediction (GBLUP) and that they are competitive with single-trait
elastic net and single-trait GBLUP in predictive performance. Finally, we discuss
their relationship with other additive-effects models and their advantages in
inference and interpretation. MAGIC populations provide an ideal setting for this
kind of investigation because the very low population structure and large sample
size result in predictive models with good power and limited confounding due to
relatedness.