Transcriptomics

Dataset Information

298

Profiling changes in gene expression by RNA-Seq during drought and recovery in switchgrass (Panicum virgatum Alamo AP13)


ABSTRACT: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light:dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses. mRNA profiles of leaf tissue from clonal replicates at various time points during drydown and recovery were generated by deep sequencing 3' mRNA tags using SOLiD.

ORGANISM(S): Panicum virgatum  

SUBMITTER: David B Lowry   Philip Fay  Thomas E Juenger  Eli Meyer  Tierney L Logan  Michael J Aspinwall  Juan D Palacio-Mejía 

PROVIDER: E-GEOD-57887 | ArrayExpress | 2014-07-01

SECONDARY ACCESSION(S): SRP042181GSE57887PRJNA248346

REPOSITORIES: GEO, ArrayExpress, ENA

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