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Edited by Ronald R. Sederoff, North Carolina State University, Raleigh, NC, and approved March 25, 2010 (received for review December 22, 2009)
Abstract
A 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.
Footnotes
- 5To whom correspondence should be addressed. E-mail: mkirst{at}ufl.edu.
Author contributions: Q.Y., C.D., B.M., and M.K. designed research; D.R.D., C.I.B., E.N., C.R.D.B.N., Q.Y., C.D., and B.M. performed research; A.B. contributed new reagents/analytic tools; D.R.D., C.I.B., A.B., E.N., J.M.M., J.Y., and M.K. analyzed data; and D.R.D., C.I.B., and M.K. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (Platform GPL7234 and Gene Expression Series GSE12623, GSE20117, and GSE20118).
This article contains supporting information online at www.pnas.org/cgi/content/full/0914709107/DCSupplemental.
Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus
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