Mapping responsive genomic elements to heat stress in a maize diversity panel

Zhikai Liang; Zachary A. Myers; Dominic Petrella; Julia Engelhorn; Thomas Hartwig; Nathan M. Springer

doi:10.1186/s13059-022-02807-7

Mapping responsive genomic elements to heat stress in a maize diversity panel

Zhikai Liang, Zachary A. Myers, Dominic Petrella, Julia Engelhorn, Thomas Hartwig, Nathan M. Springer

Research output: Contribution to journal › Article › peer-review

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Abstract

Background: Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. Results: By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Conclusions: Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.

Original language	English (US)
Article number	234
Journal	Genome biology
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s13059-022-02807-7
State	Published - Dec 2022

Bibliographical note

Funding Information:
We thank Peter Hermanson, Erika Magnusson, Chase Dickson, and Nicole Melamed for assistance with planting, phenotype measurements, and sample collections. We thank Candice Hirsch for providing a subset of seeds from the Wisconsin Diversity Panel for the experiment and Matthew Zinselmeier for kindly providing plasmids used in dual luciferase reporter assays. We thank the Minnesota Agricultural Experiment Station for providing funding for the chlorophyll fluorescence camera. We thank the Minnesota Supercomputing Institute at the University of Minnesota (http://www.msi.umn.edu) for providing resources that contributed to the research results reported within this article. The review history is available as Additional file 3. Wenjing She was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Funding Information:
This study was supported by funding from the National Science Foundation (IOS-1733633 to NMS), USDA NIFA (2021-67034-35177 to ZAM), and the German Science Foundation (DFG HA 9073 to TH).

Publisher Copyright:
© 2022, The Author(s).

Keywords

Chromatin footprints
Heat stress
Maize
Response eGene
Response eQTL

PubMed: MeSH publication types

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

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title = "Mapping responsive genomic elements to heat stress in a maize diversity panel",

abstract = "Background: Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. Results: By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Conclusions: Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.",

keywords = "Chromatin footprints, Heat stress, Maize, Response eGene, Response eQTL",

author = "Zhikai Liang and Myers, {Zachary A.} and Dominic Petrella and Julia Engelhorn and Thomas Hartwig and Springer, {Nathan M.}",

note = "Funding Information: We thank Peter Hermanson, Erika Magnusson, Chase Dickson, and Nicole Melamed for assistance with planting, phenotype measurements, and sample collections. We thank Candice Hirsch for providing a subset of seeds from the Wisconsin Diversity Panel for the experiment and Matthew Zinselmeier for kindly providing plasmids used in dual luciferase reporter assays. We thank the Minnesota Agricultural Experiment Station for providing funding for the chlorophyll fluorescence camera. We thank the Minnesota Supercomputing Institute at the University of Minnesota (http://www.msi.umn.edu) for providing resources that contributed to the research results reported within this article. The review history is available as Additional file 3. Wenjing She was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Funding Information: This study was supported by funding from the National Science Foundation (IOS-1733633 to NMS), USDA NIFA (2021-67034-35177 to ZAM), and the German Science Foundation (DFG HA 9073 to TH). Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1186/s13059-022-02807-7",

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AU - Engelhorn, Julia

AU - Hartwig, Thomas

AU - Springer, Nathan M.

N1 - Funding Information: We thank Peter Hermanson, Erika Magnusson, Chase Dickson, and Nicole Melamed for assistance with planting, phenotype measurements, and sample collections. We thank Candice Hirsch for providing a subset of seeds from the Wisconsin Diversity Panel for the experiment and Matthew Zinselmeier for kindly providing plasmids used in dual luciferase reporter assays. We thank the Minnesota Agricultural Experiment Station for providing funding for the chlorophyll fluorescence camera. We thank the Minnesota Supercomputing Institute at the University of Minnesota (http://www.msi.umn.edu) for providing resources that contributed to the research results reported within this article. The review history is available as Additional file 3. Wenjing She was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Funding Information: This study was supported by funding from the National Science Foundation (IOS-1733633 to NMS), USDA NIFA (2021-67034-35177 to ZAM), and the German Science Foundation (DFG HA 9073 to TH). Publisher Copyright: © 2022, The Author(s).

PY - 2022/12

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N2 - Background: Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. Results: By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Conclusions: Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.

AB - Background: Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. Results: By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Conclusions: Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.

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KW - Response eGene

KW - Response eQTL

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Mapping responsive genomic elements to heat stress in a maize diversity panel

Abstract

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Keywords

PubMed: MeSH publication types

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