The genomic landscape of molecular responses to natural drought stress in Panicum hallii

John T. Lovell (), Jerry Jenkins, David B. Lowry, Sujan Mamidi, Avinash Sreedasyam, Xiaoyu Weng, Kerrie Barry, Jason Bonnette, Brandon Campitelli, Chris Daum, Sean P. Gordon, Billie A. Gould, Albina Khasanova, Anna Lipzen, Alice MacQueen, Juan Diego Palacio-Mejía, Christopher Plott, Eugene V. Shakirov, Shengqiang Shu, Yuko Yoshinaga, Matt Zane, Dave Kudrna, Jason D. Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz () and Thomas E. Juenger ()
Additional contact information
John T. Lovell: HudsonAlpha Institute for Biotechnology
Jerry Jenkins: HudsonAlpha Institute for Biotechnology
David B. Lowry: Michigan State University
Sujan Mamidi: HudsonAlpha Institute for Biotechnology
Avinash Sreedasyam: HudsonAlpha Institute for Biotechnology
Xiaoyu Weng: The University of Texas at Austin
Kerrie Barry: Joint Genome Institute
Jason Bonnette: The University of Texas at Austin
Brandon Campitelli: The University of Texas at Austin
Chris Daum: Joint Genome Institute
Sean P. Gordon: Joint Genome Institute
Billie A. Gould: Michigan State University
Albina Khasanova: The University of Texas at Austin
Anna Lipzen: Joint Genome Institute
Alice MacQueen: The University of Texas at Austin
Juan Diego Palacio-Mejía: The University of Texas at Austin
Christopher Plott: HudsonAlpha Institute for Biotechnology
Eugene V. Shakirov: The University of Texas at Austin
Shengqiang Shu: Joint Genome Institute
Yuko Yoshinaga: Joint Genome Institute
Matt Zane: Joint Genome Institute
Dave Kudrna: University of Arizona
Jason D. Talag: University of Arizona
Daniel Rokhsar: University of California
Jane Grimwood: HudsonAlpha Institute for Biotechnology
Jeremy Schmutz: HudsonAlpha Institute for Biotechnology
Thomas E. Juenger: The University of Texas at Austin

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.

Date: 2018
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DOI: 10.1038/s41467-018-07669-x

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