A general Bayesian approach to analyzing diallel crosses of inbred strains.

Genetics
Alan B LenarcicWilliam Valdar

Abstract

The classic diallel takes a set of parents and produces offspring from all possible mating pairs. Phenotype values among the offspring can then be related back to their respective parentage. When the parents are diploid, sexed, and inbred, the diallel can characterize aggregate effects of genetic background on a phenotype, revealing effects of strain dosage, heterosis, parent of origin, epistasis, and sex-specific versions thereof. However, its analysis is traditionally intricate, unforgiving of unplanned missing information, and highly sensitive to imbalance, making the diallel unapproachable to many geneticists. Nonetheless, imbalanced and incomplete diallels arise frequently, albeit unintentionally, as by-products of larger-scale experiments that collect F(1) data, for example, pilot studies or multiparent breeding efforts such as the Collaborative Cross or the Arabidopsis MAGIC lines. We present a general Bayesian model for analyzing diallel data on dioecious diploid inbred strains that cleanly decomposes the observed patterns of variation into biologically intuitive components, simultaneously models and accommodates outliers, and provides shrinkage estimates of effects that automatically incorporate uncertainty due to imba...Continue Reading

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Citations

Mar 9, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Joshua N CobbSusan McCouch
Feb 22, 2012·Genetics·Karen L SvensonGary A Churchill
Nov 8, 2013·Genes and Immunity·J PhillippiJ A Frelinger
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Feb 22, 2012·Genetics·David W Threadgill, Gary A Churchill
Feb 22, 2012·Genetics·UNKNOWN Collaborative Cross Consortium
Sep 23, 2014·Genetics·Zhaojun ZhangWilliam Valdar
Dec 1, 2017·G3 : Genes - Genomes - Genetics·Sarah D TurnerPhilipp W Simon
Dec 12, 2018·PLoS Biology·Karl Grieshop, Göran Arnqvist
Mar 3, 2012·G3 : Genes - Genomes - Genetics·David W Threadgill, Gary A Churchill
Nov 7, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Andrea OnofriLuigi Russi
Aug 10, 2021·Evolution Letters·Karl GrieshopDavid Berger
Nov 6, 2021·Genetics·Rodrigo R AmadeuJeffrey B Endelman

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Methods Mentioned

BETA
X-ray

Software Mentioned

BayesDiallel
R
BayesSpike

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