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 YoshinagaMatt Zane, David A Kudrna, Jason D. Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz, Thomas E. Juenger

Research output: Contribution to journalArticle

7 Citations (Scopus)

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 C 4 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.

Original languageEnglish (US)
Article number5213
JournalNature communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018

Fingerprint

Panicum
drought
Drought
Droughts
genome
Genes
Gene Regulatory Networks
gene expression
crops
Gene expression
Crops
Genome
Gene Expression
Genetic Drift
Metagenomics
Biota
grasses
hubs
Genetic Models
loci

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Lovell, J. T., Jenkins, J., Lowry, D. B., Mamidi, S., Sreedasyam, A., Weng, X., ... Juenger, T. E. (2018). The genomic landscape of molecular responses to natural drought stress in Panicum hallii. Nature communications, 9(1), [5213]. https://doi.org/10.1038/s41467-018-07669-x

The genomic landscape of molecular responses to natural drought stress in Panicum hallii. / Lovell, John T.; Jenkins, Jerry; Lowry, David B.; Mamidi, Sujan; Sreedasyam, Avinash; Weng, Xiaoyu; Barry, Kerrie; Bonnette, Jason; Campitelli, Brandon; Daum, Chris; Gordon, Sean P.; Gould, Billie A.; Khasanova, Albina; Lipzen, Anna; MacQueen, Alice; Palacio-Mejía, Juan Diego; Plott, Christopher; Shakirov, Eugene V.; Shu, Shengqiang; Yoshinaga, Yuko; Zane, Matt; Kudrna, David A; Talag, Jason D.; Rokhsar, Daniel; Grimwood, Jane; Schmutz, Jeremy; Juenger, Thomas E.

In: Nature communications, Vol. 9, No. 1, 5213, 01.12.2018.

Research output: Contribution to journalArticle

Lovell, JT, Jenkins, J, Lowry, DB, Mamidi, S, Sreedasyam, A, Weng, X, Barry, K, Bonnette, J, Campitelli, B, Daum, C, Gordon, SP, Gould, BA, Khasanova, A, Lipzen, A, MacQueen, A, Palacio-Mejía, JD, Plott, C, Shakirov, EV, Shu, S, Yoshinaga, Y, Zane, M, Kudrna, DA, Talag, JD, Rokhsar, D, Grimwood, J, Schmutz, J & Juenger, TE 2018, 'The genomic landscape of molecular responses to natural drought stress in Panicum hallii', Nature communications, vol. 9, no. 1, 5213. https://doi.org/10.1038/s41467-018-07669-x
Lovell, John T. ; Jenkins, Jerry ; Lowry, David B. ; Mamidi, Sujan ; Sreedasyam, Avinash ; Weng, Xiaoyu ; Barry, Kerrie ; Bonnette, Jason ; Campitelli, Brandon ; Daum, Chris ; Gordon, Sean P. ; Gould, Billie A. ; Khasanova, Albina ; Lipzen, Anna ; MacQueen, Alice ; Palacio-Mejía, Juan Diego ; Plott, Christopher ; Shakirov, Eugene V. ; Shu, Shengqiang ; Yoshinaga, Yuko ; Zane, Matt ; Kudrna, David A ; Talag, Jason D. ; Rokhsar, Daniel ; Grimwood, Jane ; Schmutz, Jeremy ; Juenger, Thomas E. / The genomic landscape of molecular responses to natural drought stress in Panicum hallii. In: Nature communications. 2018 ; Vol. 9, No. 1.
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