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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND MOLECULAR APPROACHES TO WHEAT TRAITS

Location: Genomics and Gene Discovery

Title: Systems genetics of environmental response in the mature wheat embryo

Authors
item Munkvold, Jesse -
item L Chingcuanco, Debbie
item Sorrells, Mark -

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 26, 2013
Publication Date: March 11, 2013
Citation: Munkvold, J.D., Chingcuanco, D.L., Sorrells, M. 2013. Systems genetics of environmental response in the mature wheat embryo. Genetics. doi:10.1534/genetics.113.150052.

Interpretive Summary: The comparative Weighted Gene Co-Expression Network Analysis was used to compare the influence of different growing environments on gene co-expression in the mature wheat embryo. This network approach was combined with the mapping of individual gene expression quantitative trait loci (eQTL) to examine the genetic control of environmentally static and variable gene expression. This procedure identified conserved co-regulation of gene expression between environments related to basic developmental and cellular functions.

Technical Abstract: Quantitative phenotypic traits are influenced by genetic and environmental variables as well as the interaction between the two. Underlying genetic x environment interaction is the influence the surrounding environment exerts on gene expression. Perturbation of gene expression by environmental factors manifests itself in alterations to gene co-expression networks and ultimately in phenotypic plasticity. Recently comparative gene co-expression networks have been used to uncover biological mechanisms that differentiate tissues or other biological factors. In this study we have extended comparative Weighted Gene Co-Expression Network Analysis to compare the influence of different growing environments on gene co-expression in the mature wheat (Triticum aestivum) embryo. This network approach was combined with the mapping of individual gene expression QTL to examine the genetic control of environmentally static and variable gene expression. The presented approach is useful for gene expression experiments containing multiple environments and allowed for the identification of specific gene co-expression modules responsive to environmental factors. This procedure identified conserved co-regulation of gene expression between environments related to basic developmental and cellular functions including protein localization and catabolism, vesicle composition/trafficking, golgi transport, and polysaccharide metabolism, among others. Environmentally unique modules were found to contain genes with predicted functions in responding to abiotic and biotic environmental variables. These findings represent the first report using a Weighted Gene Co-expression Network Analysis approach to characterize the influence of environment on coordinated transcriptional regulation.

Last Modified: 9/20/2014
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