@article{e0ca97270bf849afb65a048887ef2306,
title = "The genomic landscape of molecular responses to natural drought stress in Panicum hallii",
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.",
author = "Lovell, {John T.} and Jerry Jenkins and Lowry, {David B.} and Sujan Mamidi and Avinash Sreedasyam and Xiaoyu Weng and Kerrie Barry and Jason Bonnette and Brandon Campitelli and Chris Daum and Gordon, {Sean P.} and Gould, {Billie A.} and Albina Khasanova and Anna Lipzen and Alice MacQueen and Palacio-Mej{\'i}a, {Juan Diego} and Christopher Plott and Shakirov, {Eugene V.} and Shengqiang Shu and Yuko Yoshinaga and Matt Zane and Dave Kudrna and Talag, {Jason D.} and Daniel Rokhsar and Jane Grimwood and Jeremy Schmutz and Juenger, {Thomas E.}",
note = "Funding Information: This project is the result of nearly a decade of field and laboratory work, which was accomplished with the help of J. Heiling, A. Asmus, C. Purmal, D. Des Marais, J. Reilley, T.S. Quedensley, B. Whitaker, K. Hernandez, E. Milano, M.J. Aspinwall, S.H. Taylor, and other members of the Juenger lab at UT Austin. We thank the UT Brackenridge Field Lab and the Ladybird Johnson Wildflower Center for providing support and field sites for experiments. Y. Stuart, S. Sen, K. Broman, D. Hoover, R. Williamson, R. Holmer, E. Schranz, and D. Bolnick provided advice on methods and presentation. Computational analyses were conducted, in part, on the Stampede system with allocations from the Texas Advance Computing Center. We thank Dan Sisco and Bill LaRochelle from 454/ Roche for early data contributions to the filipes reference and Michael Kertesz for early access to Moleculo library technology. We thank collaborators at the Donald Danforth Center and the Joint Genome Institute for access to the prepublication genome and annotation of Seteria viridis to use in the outgroup analysis. This work was funded by NSF/IOS-1402393 (J.T.L.), NSF/IOS-1639872 (J.T.L./T.E.J.), NSF/IOS-0922457 (T.E.J.), NSF/IOS-1444533 (T.E.J.), DOE/DE-SC0008451 (T.E.J.), DOE/DE-SC0018409 (D.B.L.), DOE/DE-FC02-07ER64494 (D.B.L.), and USDA/NIFA 2011-67012-309969 (D.B.L.). E. V.S. was supported in part by the Russian Government Program of Competitive Growth of Kazan Federal University. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Publisher Copyright: {\textcopyright} 2018, The Author(s).",
year = "2018",
month = dec,
day = "1",
doi = "10.1038/s41467-018-07669-x",
language = "English (US)",
volume = "9",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}