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Research Project: Discovery of Plant Genetic Mechanisms Controlling Microbial Recruitment to the Root Microbiome

Location: Plant Gene Expression Center

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

Author
item VAROQUAUX, NELLE - University Of California
item COLE, BENJAMIN - Joint Genome Institute
item GAO, CHENG - University Of California
item PIERROZ, GRADY - University Of California
item BAKER, CHRISTOPHER - University Of California
item PATEL, DHRUV - University Of California
item MADERA, MARY - University Of California
item JEFFERS, TIM - University Of California
item HOLLINGSWORTH, JOY - Kearney Agricultural Center
item SIEVERT, JULIE - Kearney Agricultural Center
item YOSHINAGA, YUKO - University Of California
item OWITI, JUDITH - University Of California
item SINGAN, VASANTH - Joint Genome Institute
item DEGRAAF, STEPHANIE - University Of California
item XU, LING - University Of California
item BLOW, MATTHEW - Joint Genome Institute
item HARRISON, MARIA - University Of California
item VISEL, AXEL - Joint Genome Institute
item JANSSON, CHRISTER - Pacific Northwest National Laboratory
item NIYOGI, KRISHNA - University Of California
item HUTMACHER, ROBERT - Kearney Agricultural Center
item Coleman-Derr, Devin
item O'MALLEY, RONAN - Joint Genome Institute
item TAYLOR, JOHN - University Of California
item DAHLBERG, JEFFREY - Kearney Agricultural Center
item VOGEL, JOHN - Joint Genome Institute
item LEMAUX, PEGGY - University Of California
item PURDOM, ELIZABETH - University Of California

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/31/2019
Publication Date: 12/26/2019
Citation: Varoquaux, N., Cole, B., Gao, C., Pierroz, G., Baker, C., Patel, D., Madera, M., Jeffers, T., Hollingsworth, J., Sievert, J., Yoshinaga, Y., Owiti, J., Singan, V., Degraaf, S., Xu, L., Blow, M., Harrison, M., Visel, A., Jansson, C., Niyogi, K., Hutmacher, R., Coleman-Derr, D.A., O'Malley, R., Taylor, J., Dahlberg, J., Vogel, J., Lemaux, P., Purdom, E. 2019. Transcriptomic analysis of field-droughted sorghum from seeding to maturity reveals biotic and metabolic responses. Proceedings of the National Academy of Sciences. 116(52):27124–27132. https://doi.org/10.1073/pnas.1907500116.
DOI: https://doi.org/10.1073/pnas.1907500116

Interpretive Summary: Drought dramatically impacts crop growth and productivity, causing losses estimated at 2.9 billion dollars annually. While the physiological responses of plants to drought have been extensively studied in model organisms under controlled laboratory or greenhouse conditions, results from these studies typically translate poorly to field-grown plants, suggesting a complex interaction between environmental factors and drought responses. Thus, a better mechanistic understanding of drought responses in the field is needed to developeffective drought mitigation strategies.

Technical Abstract: Here we provide the first field-based, temporal transcriptomic study of sorghum. We profiled over 350 transcriptomes sampled weekly from leaves and roots, two genotypes (the pre-flowering drought tolerantRTx430 and the stay-green type BTx642), under control watering and two different drought regimes. We present here the first transcriptomic study to look at the recovery from pre-flowering drought, by reintroducing water after anthesis, and the effects of post-flowering drought, by removing water after anthesis. Our weekly time series reveals that within a week of drought exposure sorghum detects and adapts to pre-and post-flowering drought stresses, ultimately influencing the gene expression of over 40% of the genome. This transcriptomic response includes genes involved in critical functions, such as biotic defense and abiotic stress responses, and photosynthesis. We demonstrate that the stay-green genotype, BTx642, maintains high levels of photosynthetic gene expression during post-flowering drought, compared to RTx430. This study is the largest transcriptome survey of field-grown sorghum, and, paired with soil, rhizosphere, and root microbiomes, represents an unparalleled resource for studying drought tolerance in agronomically-relevant settings.