title: Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass.
abstract: Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass,Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with transeffects.Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% oft rans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and transregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA;
authors.forename: John T
authors.initials: JT
authors.lastname: Lovell
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA;
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.affiliation: Department of Plant Sciences, Michigan State University, East Lansing, Michigan 48824, USA;
authors.forename: David B
authors.initials: DB
authors.lastname: Lowry
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 42008, Republic of Tatarstan, Russia;
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Shakirov
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA;
authors.forename: Jason E
authors.initials: JE
authors.lastname: Bonnette
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA;
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Weng
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
authors.forename: Jenifer
authors.initials: J
authors.lastname: Johnson
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.
authors.forename: Avinash
authors.initials: A
authors.lastname: Sreedasyam
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Plott
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA;
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Juenger
mesh_terms: D000483:Alleles; D002980:Climate; D055864:Droughts; D060146:Ecotype; D018506:Gene Expression Regulation, Plant; D059647:Gene-Environment Interaction; D017343:Genes, Plant; D005838:Genotype; D006824:Hybridization, Genetic; D006109:Poaceae / Q000235:genetics*