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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #320178

Research Project: Characterizing Circadian Regulatory Networks in Grain Crops to Establish their Role in Development and Abiotic Responses

Location: Plant Gene Expression Center

Title: Daytime soybean transcriptome fluctuations during water deficit stress

Author
item RODRIGUES, F - EMBRAPA
item FUGANTI-PAGLIARINI, R - EMBRAPA
item GOMES, J - EMBRAPA
item NAKAYAMA, THIAGO - EMBRAPA
item MOLINARI, HUGO BRUNO - EMBRAPA
item LOBO, FRANCISCO - EMBRAPA
item Harmon, Frank
item NEPOMUCENO, ALEXANDRE - EMBRAPA

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/26/2015
Publication Date: 6/26/2015
Citation: Rodrigues, F.A., Fuganti-Pagliarini, R., Gomes, J.M., Nakayama, T.J., Molinari, H.C., Lobo, F.P., Harmon, F.G., Nepomuceno, A.L. 2015. Daytime soybean transcriptome fluctuations during water deficit stress. BMC Genomics. 16:505. doi:10.1186/s12864-015-1731-x.

Interpretive Summary: Drought seriously affects soybean growth and development, yet the full extent of the drought stress-acclimation response in this important crop species is incompletely understood. To better understand how soybean plants adapt to drought stress, we examined the dynamic changes in gene expression induced by drought. We identified nearly five thousand genes that had changed expression after exposure to water deficit. As expected based on previous work in other plant species, a large proportion of gene expression in control plants not exposed to drought stress had daily rhythmic expression patterns, which are controlled by internal signaling pathways like the circadian clock and external environmental cues. Thus, gene expression changes during normal development through the day and night. Overall differences in this rhythmic gene expression in plants under stress compared to unstressed plants were primarily observed in early morning to late day. Genes known to be associated with stress response pathways were triggered primarily during midday, in which case more genes were upregulated compared to early morning. Additionally, genes known to be involved in secondary metabolism and hormone signaling were changed by drought stress and these were mainly expressed at night. This study demonstrates that gene expression networks are dynamically shaped to acclimate plant metabolism to stressful environmental conditions. We have identified genes with rhythmic diurnal expression that are expressed in soybean leaves under normal developmental conditions and genes whose expression oscillates under conditions of water deficit. These results show that time of day-dependent regulation, as well as changes in light and temperature, have a substantial impact on soybean response to drought.

Technical Abstract: Since drought can seriously affect plant growth and development and little is known about how the oscillations of gene expression during the drought stress-acclimation response in soybean is affected, we applied Illumina technology to sequence 36 cDNA libraries synthesized from control and drought-stressed soybean plants to verify the dynamic changes in gene expression during a 24-h time course. Cycling variables were measured from the expression data to determine the putative circadian rhythm regulation of gene expression. We identified 4866 genes differentially expressed in soybean plants in response to water deficit. Of these genes, 3715 were differentially expressed during the light period, from which approximately 9.55 % were observed in both light and darkness. We found 887 genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes, 35.52 % exhibited expression oscillations in a 24 h period. This number increased to 39.23 % when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Such differences in plants under stress were primarily observed in ZT0 (early morning) to ZT8 (late day) and also from ZT4 to ZT12. Stress-related pathways were triggered in response to water deficit primarily during midday, when more genes were upregulated compared to early morning. Additionally, genes known to be involved in secondary metabolism and hormone signaling were also expressed in the dark period. Gene expression networks can be dynamically shaped to acclimate plant metabolism under environmental stressful conditions. We have identified putative cycling genes that are expressed in soybean leaves under normal developmental conditions and genes whose expression oscillates under conditions of water deficit. These results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.