Dataset Information

DesignGG: an R-package and web tool for the optimal design of genetical genomics experiments.

ABSTRACT:

Background

High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological systems. The optimal design of such genetical genomics experiments in a cost-efficient and effective way is not trivial.

Results

This paper presents designGG, an R package for designing optimal genetical genomics experiments. A web implementation for designGG is available at http://gbic.biol.rug.nl/designGG. All software, including source code and documentation, is freely available.

Conclusion

DesignGG allows users to intelligently select and allocate individuals to experimental units and conditions such as drug treatment. The user can maximize the power and resolution of detecting genetic, environmental and interaction effects in a genome-wide or local mode by giving more weight to genome regions of special interest, such as previously detected phenotypic quantitative trait loci. This will help to achieve high power and more accurate estimates of the effects of interesting factors, and thus yield a more reliable biological interpretation of data. DesignGG is applicable to linkage analysis of experimental crosses, e.g. recombinant inbred lines, as well as to association analysis of natural populations.

SUBMITTER: Li Y

PROVIDER: S-EPMC2706229 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

designGG: an R-package and web tool for the optimal design of genetical genomics experiments.

Li Yang Y Swertz Morris A MA Vera Gonzalo G Fu Jingyuan J Breitling Rainer R Jansen Ritsert C RC

BMC bioinformatics 20090618

<h4>Background</h4>High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological systems. The optimal design of such genetical genomics experiments in a cost-efficient and effective way is not trivial.<h4>Results</h4>This paper presents designGG, an R package for designing optimal genetical genomics experiments. A web implementation for designGG is availa ...[more]

PMID: 19538731

Similar Datasets

Project description:BackgroundLeaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree to identify genetic factors controlling leaf shape. The approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.ResultsA major QTL for leaf lamina width and length:width ratio was identified in multiple experiments that confirmed its stability. A transcriptome analysis of expanding leaf tissue contrasted gene expression between individuals with alternative QTL alleles, and identified an ADP-ribosylation factor (ARF) GTPase (PtARF1) as a candidate gene for regulating leaf morphology in this pedigree. ARF GTPases are critical elements in the vesicular trafficking machinery. Disruption of the vesicular trafficking function of ARF by the pharmacological agent Brefeldin A (BFA) altered leaf lateral growth in the narrow-leaf P. trichocarpa suggesting a molecular mechanism of leaf shape determination. Inhibition of the vesicular trafficking processes by BFA interferes with cycling of PIN proteins and causes their accumulation in intercellular compartments abolishing polar localization and disrupting normal auxin flux with potential effects on leaf expansion.ConclusionsIn other model systems, ARF proteins have been shown to control the localization of auxin efflux carriers, which function to establish auxin gradients and apical-basal cell polarity in developing plant organs. Our results support a model where PtARF1 transcript abundance changes the dynamics of endocytosis-mediated PIN localization in leaf cells, thus affecting lateral auxin flux and subsequently lamina leaf expansion. This suggests that evolution of differential cellular polarity plays a significant role in leaf morphological variation observed in subgenera of genus Populus.