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

Nelle Varoquaux; Benjamin Cole; Cheng Gao; Grady Pierroz; Christopher R Baker; Dhruv Patel; Mary Madera; Tim Jeffers; Joy Hollingsworth; Julie Sievert; Yuko Yoshinaga; Judith A Owiti; Vasanth R Singan; Stephanie DeGraaf; Ling Xu; Matthew J Blow; Maria J Harrison; Axel Visel; Christer Jansson; Krishna K Niyogi; Robert Hutmacher; Devin Coleman-Derr; Ronan C O'Malley; John W Taylor; Jeffery Dahlberg; John P Vogel; Peggy G Lemaux; Elizabeth Purdom

doi:10.1073/pnas.1907500116

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

Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):27124-27132. doi: 10.1073/pnas.1907500116. Epub 2019 Dec 5.

Authors

Nelle Varoquaux^{1

2}, Benjamin Cole³, Cheng Gao⁴, Grady Pierroz^{4

5}, Christopher R Baker^{4

6}, Dhruv Patel^{4

6}, Mary Madera⁴, Tim Jeffers^{4

6}, Joy Hollingsworth⁷, Julie Sievert⁷, Yuko Yoshinaga³, Judith A Owiti⁴, Vasanth R Singan³, Stephanie DeGraaf¹, Ling Xu^{4

5}, Matthew J Blow³, Maria J Harrison⁸, Axel Visel^{3

9

10}, Christer Jansson¹¹, Krishna K Niyogi^{4

6

12}, Robert Hutmacher^{13

14}, Devin Coleman-Derr^{4

5}, Ronan C O'Malley³, John W Taylor⁴, Jeffery Dahlberg⁷, John P Vogel^{3

4

9}, Peggy G Lemaux⁴, Elizabeth Purdom¹

Affiliations

¹ Department of Statistics, University of California, Berkeley, CA 94720.
² Berkeley Institute for Data Science, University of California, Berkeley, CA 94720.
³ Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
⁴ Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720.
⁵ Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710.
⁶ Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.
⁷ Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources, Parlier, CA 93648.
⁸ Boyce Thompson Institute, Ithaca, NY 14853.
⁹ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
¹⁰ School of Natural Sciences, University of California, Merced, CA 95343.
¹¹ Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352.
¹² Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
¹³ West Side Research and Extension Center, University of California, Five Points, CA 93624.
¹⁴ Department of Plant Sciences, University of California, Davis, 95616.

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.

Keywords: RNA-Seq; S. bicolor; arbuscular mycorrhizal fungi; drought.