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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, Dave, Talag, Jason D., Rokhsar, Daniel, Grimwood, Jane, Schmutz, Jeremy, Juenger, Thomas E.·2018·Nature Communications
DOI 10.1038/s41467-018-07669-xPMC PMC6283873
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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.

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  • GENESPACE was originally designed to solve the problem between the two P. hallii reference genomes and their F2 progeny using synteny to project the positions of genes across multiple genomes onto the physical positions of a reference.

    “GENESPACE is ideally suited for this type of exploration, and indeed was originally designed to solve this problem between the two P. hallii reference genomes and their F2 progeny (Lovell et al., 2018) using synteny to project the positions of genes across multiple genomes onto the physical positions of a reference.”

    From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as Lovell et al., 2018

    The Results section, “Development and comparison of two complete de novo genomes” (page unavailable), identifies GENESPACE as the authors’ pipeline for comparing the HAL2 and FIL2 genomes using synteny-constrained gene networks. The Methods section, “Comparative genomics” (page unavailable), describes orthology inference within syntenic blocks, but does not say the pipeline was designed to project gene positions onto a reference or to solve a problem involving the F2 progeny. The paper describes F2 genetic-map construction separately. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • By exploring only syntenic orthologs it is possible to examine all putatively functional variants within a genomic region of interest, even those in genes that are absent in the focal reference genome.

    “For example, by exploring only syntenic orthologs it is possible to examine all putatively functional variants within a genomic region of interest, even those in genes that are absent in the focal reference genome (Lovell et al., 2018).”

    From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as Lovell et al., 2018

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Metadata

Authors
Lovell, J. T., Jenkins, J., Lowry, D. B., Mamidi, S., Sreedasyam, A., Weng, X., Barry, K., Bonnette, J., Campitelli, B., Daum, C., Gordon, S. P., Gould, B. A., Khasanova, A., Lipzen, A., MacQueen, A., Palacio-Mejía, J. D., Plott, C., Shakirov, E. V., Shu, S., Yoshinaga, Y., Zane, M., Kudrna, D., Talag, J. D., Rokhsar, D., Grimwood, J., Schmutz, J., & Juenger, T. E.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2018-12-06
Volume
9
Issue
1
ISSN
2041-1723
DOI
10.1038/s41467-018-07669-x
PMC
PMC6283873
Cited by
135
References
1
Language
en
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