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Title: Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses

Abstract

Drought is the most important environmental stress limiting crop yields. The C4 cereal sorghum [ Sorghum bicolor (L.) Moench] is a critical food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing preflowering and postflowering drought stress on 2 genotypes of sorghum across a tightly resolved time series, from plant emergence to postanthesis, resulting in a dataset of nearly 400 transcriptomes. We observed a fast and global transcriptomic response in leaf and root tissues with clear temporal patterns, including modulation of well-known drought pathways. We also identified genotypic differences in core photosynthesis and reactive oxygen species scavenging pathways, highlighting possible mechanisms of drought tolerance and of the delayed senescence, characteristic of the stay-green phenotype. Finally, we discovered a large-scale depletion in the expression of genes critical to arbuscular mycorrhizal (AM) symbiosis, with a corresponding drop in AM fungal mass in the plants’ roots.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1];  [3];  [1]; ORCiD logo [1];  [1];  [1];  [4];  [4]; ORCiD logo [2];  [1];  [2];  [1];  [3];  [2];  [5];  [6]; ORCiD logo [7]; ORCiD logo [8] more »;  [9];  [3];  [2];  [1];  [4]; ORCiD logo [10];  [1]; ORCiD logo [1] « less
  1. Univ. of California, Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. of California, Berkeley, CA (United States); US Department of Agriculture–Agricultural Research Service, Albany, CA (United States)
  4. Univ. of California Agriculture and Natural Resources, Parlier, CA (United States)
  5. Boyce Thompson Inst., Ithaca, NY (United States)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Merced, CA (United States)
  7. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  8. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  9. Univ. of California, Five Points, CA (United States); Univ. of California, Davis, CA (United States)
  10. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1577228
Alternate Identifier(s):
OSTI ID: 1582406
Report Number(s):
PNNL-SA-140530
Journal ID: ISSN 0027-8424
Grant/Contract Number:  
AC05-76RL01830; SC0012460; SC0014081; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 116; Journal Issue: 52; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; drought; RNA-Seq; S. bicolorarbuscular mycorrhizal fungi

Citation Formats

Varoquaux, Nelle, Cole, Benjamin, Gao, Cheng, Pierroz, Grady, Baker, Christopher R., Patel, Dhruv, Madera, Mary, Jeffers, Tim, Hollingsworth, Joy, Sievert, Julie, Yoshinaga, Yuko, Owiti, Judith A., Singan, Vasanth R., DeGraaf, Stephanie, Xu, Ling, Blow, Matthew J., Harrison, Maria J., Visel, Axel, Jansson, Christer, Niyogi, Krishna K., Hutmacher, Robert, Coleman-Derr, Devin, O’Malley, Ronan C., Taylor, John W., Dahlberg, Jeffery, Vogel, John P., Lemaux, Peggy G., and Purdom, Elizabeth. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. United States: N. p., 2019. Web. doi:10.1073/pnas.1907500116.
Varoquaux, Nelle, Cole, Benjamin, Gao, Cheng, Pierroz, Grady, Baker, Christopher R., Patel, Dhruv, Madera, Mary, Jeffers, Tim, Hollingsworth, Joy, Sievert, Julie, Yoshinaga, Yuko, Owiti, Judith A., Singan, Vasanth R., DeGraaf, Stephanie, Xu, Ling, Blow, Matthew J., Harrison, Maria J., Visel, Axel, Jansson, Christer, Niyogi, Krishna K., Hutmacher, Robert, Coleman-Derr, Devin, O’Malley, Ronan C., Taylor, John W., Dahlberg, Jeffery, Vogel, John P., Lemaux, Peggy G., & Purdom, Elizabeth. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. United States. doi:10.1073/pnas.1907500116.
Varoquaux, Nelle, Cole, Benjamin, Gao, Cheng, Pierroz, Grady, Baker, Christopher R., Patel, Dhruv, Madera, Mary, Jeffers, Tim, Hollingsworth, Joy, Sievert, Julie, Yoshinaga, Yuko, Owiti, Judith A., Singan, Vasanth R., DeGraaf, Stephanie, Xu, Ling, Blow, Matthew J., Harrison, Maria J., Visel, Axel, Jansson, Christer, Niyogi, Krishna K., Hutmacher, Robert, Coleman-Derr, Devin, O’Malley, Ronan C., Taylor, John W., Dahlberg, Jeffery, Vogel, John P., Lemaux, Peggy G., and Purdom, Elizabeth. Thu . "Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses". United States. doi:10.1073/pnas.1907500116.
@article{osti_1577228,
title = {Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses},
author = {Varoquaux, Nelle and Cole, Benjamin and Gao, Cheng and Pierroz, Grady and Baker, Christopher R. and Patel, Dhruv and Madera, Mary and Jeffers, Tim and Hollingsworth, Joy and Sievert, Julie and Yoshinaga, Yuko and Owiti, Judith A. and Singan, Vasanth R. and DeGraaf, Stephanie and Xu, Ling and Blow, Matthew J. and Harrison, Maria J. and Visel, Axel and Jansson, Christer and Niyogi, Krishna K. and Hutmacher, Robert and Coleman-Derr, Devin and O’Malley, Ronan C. and Taylor, John W. and Dahlberg, Jeffery and Vogel, John P. and Lemaux, Peggy G. and Purdom, Elizabeth},
abstractNote = {Drought is the most important environmental stress limiting crop yields. The C4 cereal sorghum [ Sorghum bicolor (L.) Moench] is a critical food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing preflowering and postflowering drought stress on 2 genotypes of sorghum across a tightly resolved time series, from plant emergence to postanthesis, resulting in a dataset of nearly 400 transcriptomes. We observed a fast and global transcriptomic response in leaf and root tissues with clear temporal patterns, including modulation of well-known drought pathways. We also identified genotypic differences in core photosynthesis and reactive oxygen species scavenging pathways, highlighting possible mechanisms of drought tolerance and of the delayed senescence, characteristic of the stay-green phenotype. Finally, we discovered a large-scale depletion in the expression of genes critical to arbuscular mycorrhizal (AM) symbiosis, with a corresponding drop in AM fungal mass in the plants’ roots.},
doi = {10.1073/pnas.1907500116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 52,
volume = 116,
place = {United States},
year = {2019},
month = {12}
}

Journal Article:
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DOI: 10.1073/pnas.1907500116

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