Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus
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Data
2010
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Resumo
fundamental goal of systems biology is to identify genetic
elements that contribute to complex phenotypes and to understand
how they interact in networks predictive of system response
to genetic variation. Few studies in plants have developed such
networks, and none have examined their conservation among
functionally specialized organs. Here we used genetical genomics
in an interspecific hybrid population of the model hardwood plant
Populus to uncover transcriptional networks in xylem, leaves, and
roots. Pleiotropic eQTL hotspots were detected and used to construct
coexpression networks a posteriori, for which regulators
were predicted based on cis-acting expression regulation. Networks
were shown to be enriched for groups of genes that function
in biologically coherent processes and for cis-acting promoter
motifs with known roles in regulating common groups of genes.
When contrasted among xylem, leaves, and roots, transcriptional
networks were frequently conserved in composition, but almost
invariably regulated by different loci. Similarly, the genetic architecture
of gene expression regulation is highly diversified among
plant organs, with less than one-third of genes with eQTL detected
in two organs being regulated by the same locus. However, colocalization
in eQTL position increases to 50% when they are detected
in all three organs, suggesting conservation in the genetic
regulation is a function of ubiquitous expression. Genes conserved
in their genetic regulation among all organs are primarily cis regulated
(∼92%), whereas genes with eQTL in only one organ are
largely trans regulated. Trans-acting regulation may therefore
be the primary driver of differentiation in function between
plant organs.
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Palavras-chave
eQTL, Populus, Gene network, Gene regulation, Systems biology
Citação
DROST, Derek R. et al. Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of ppulus. Proceedings of the National Academy of Sciences of the United States of America, Washington, v. 107, n. 18, p. 8492-8497, 2010.