Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses

Authors: HAYFORD, RITA - Delaware State University; Serba, Desalegn; XIE, SHAOJUN - Purdue University; AYYAPPAN, VASUDEVAN - University Of Delaware; THIMMAPURAM, JYOTHI - Purdue University; SAHA, MALAY - Noble Research Institute; WU, CATHY - University Of Delaware; KALAVACHARLA, VENU - Delaware State University

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/10/2022
Publication Date: 3/8/2022
Citation: Hayford, R.K., Serba, D.D., Xie, S., Ayyappan, V., Thimmapuram, J., Saha, M.C., Wu, C.H., Kalavacharla, V. 2022. Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses. Biomed Central (BMC) Plant Biology. 22. Article 107. https://doi.org/10.1186/s12870-022-03477-0.
DOI: https://doi.org/10.1186/s12870-022-03477-0

Interpretive Summary: Sustainable production of high-quality switchgrass feedstock in marginal areas has been of great interest in cellulosic bioenergy research. Understanding the effects of drought and high temperatures on switchgrass productivity are key to sustainability. That understanding needs to be based on knowledge at the molecular level and on the controlling genes. However, there is very little knowledge about which genes, and how many of them, are important for heat and drought tolerance. This study was conducted on one variety, Alamo (AP13) to help answer these questions. By imposing heat and drought stress under controlled environments, we were able to identify genes responsive to individual and combined stresses. We found 3,912 genes to be drought (DT) responsive, 2,339 heat (HT) responsive, and 4,635 combined drought and heat (DTHT) stress responsive. These genes help the plant overcome physiological damage caused by water deficit and maintain growth and development. Some of these genes reinforce stem strength to overcome individual as well as combined stresses. Findings from this study are important for breeders to deploy stress responsive genes in a cultivar and researchers seeking bioenergy crops that are stress tolerant.

Technical Abstract: Background: Sustainable production of high-quality feedstock has been of great interest in bioenergy research. Despite the economic importance, high temperatures and water deficit are limiting factors for the successful cultivation of switchgrass in semi-arid areas. There are limited reports on the molecular basis of combined abiotic stress tolerance in switchgrass, particularly the combination of drought and heat stress. We used transcriptomic approaches to elucidate the changes in the response of switchgrass to drought and high temperature simultaneously. Results: We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night)was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted. Out of a total of 32,190 genes, we identified 3,912, as DT responsive genes, 2,339 and 4,635 as , heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively. Gene ontology annotation identified the metabolic process as the significant term enriched in DTHT genes. Other biological processes identified in DTHT responsive genes included: response to water, photosynthesis, oxidation-reduction processes, and response to stress. KEGG pathway enrichment analysis on DT and DTHT responsive genes revealed that TFs and genes controlling phenylpropanoid pathways were important for individual as well as combined stress response. For example, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) from the phenylpropanoid pathway was induced by single DT and combinations of DTHT stress. Conclusion: Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.