ArticleProceedings of the National Academy of Sciences of the United States of America2010
Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 63 citations in OpenAlex.
- Variation in flooding tolerance in Populus deltoides 'D-124' and P. trichocarpa × P. deltoides hybrid '52-225'.Tree physiology · 2025Article
- eQTLs play critical roles in regulating gene expression and identifying key regulators in rice.Plant biotechnology journal · 2022Article
- Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).Scientific reports · 2022Article
- Genetic Architecture Underlying the Metabolites of Chlorogenic Acid Biosynthesis inInternational journal of molecular sciences · 2021Article
- The uncharacterized geneProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Xylan in the Middle: Understanding Xylan Biosynthesis and Its Metabolic Dependencies Toward Improving Wood Fiber for Industrial Processing.Frontiers in plant science · 2019Review
- Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks.Frontiers in plant science · 2019Review
- Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus.Plant biotechnology journal · 2019Article
- Gene co-expression network connectivity is an important determinant of selective constraint.PLoS genetics · 2017Article
- eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice.Frontiers in plant science · 2017Article
- Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus.BMC plant biology · 2016Article
- Learning from Co-expression Networks: Possibilities and Challenges.Frontiers in plant science · 2016Review
- Genetical genomics of Populus leaf shape variation.BMC plant biology · 2015Article
- High-level expression of sugar inducible gene2 (HSI2) is a negative regulator of drought stress tolerance in Arabidopsis.BMC plant biology · 2013Article
- Navigating the transcriptional roadmap regulating plant secondary cell wall deposition.Frontiers in plant science · 2013Review
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- Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla.BMC genetics · 2012Article
- Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population.BMC plant biology · 2012Article
- Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce.PloS one · 2012Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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 (approximately 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.