Transcriptome analysis of heat stress response in switchgrass (Panicum virgatumL.)

Abstract

BackgroundGlobal warming predictions indicate that temperatures will increase by another 2-6°C by the end of this century. High temperature is a major abiotic stress limiting plant growth and productivity in many areas of the world. Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop, due to its rapid growth rate, reliable biomass yield, minimal requirements of water and nutrients, adaptability to grow on marginal lands and widespread distribution throughout North America. The effect of high temperature on switchgrass physiology, cell wall composition and biomass yields has been reported. However, there is void in the knowledge of the molecular responses to heat stress in switchgrass.ResultsWe conducted long-term heat stress treatment (38°/30°C, day/night, for 50 days) in the switchgrass cultivar Alamo. A significant decrease in the plant height and total biomass was evident in the heat stressed plants compared to controls. Total RNA from control and heat stress samples were used for transcriptome analysis with switchgrass Affymetrix genechips. Following normalization and pre-processing, 5365 probesets were identified as differentially expressed using a 2-fold cutoff. Of these, 2233 probesets (2000 switchgrass unigenes) were up-regulated, and 3132 probesets (2809 unigenes) were down-regulated. Differential expression of 42 randomly selected genes from this list was validated using RT-PCR. Rice orthologs were retrieved for 78.7% of the heat stress responsive switchgrass probesets. Gene ontology (GOs) enrichment analysis using AgriGO program showed that genes related to ATPase regulator, chaperone binding, and protein folding was significantly up-regulated. GOs associated with protein modification, transcription, phosphorus and nitrogen metabolic processes, were significantly down-regulated by heat stress.ConclusionsPlausible connections were identified between the identified GOs, physiological responses and heat response phenotype observed in switchgrass plants. Comparative transcriptome analysis in response to heat stress among four monocots – switchgrass, rice, wheat and maize identified 16 common genes, most of which were associated with protein refolding processes. These core genes will be valuable biomarkers for identifying heat sensitive plant germplasm since they are responsive to both short duration as well as chronic heat stress treatments, and are also expressed in different plant growth stages and tissue types.

Senescence, dormancy and tillering in perennial C4 grasses

“…These studies served as a bridge to the current sequencing and annotation of the switchgrass genome available at www.phytozome.org [114], the use of microarrays [115,116], and next generation sequencing [42,117] for understanding different aspects of plant development and responses to the environment. Parallel work on the genetics and genomics of switchgrass has resulted in a deeper understanding of genome organization, linkage groups, single nucleotide polymorphisms (SNPs) and molecular markers associated with specific linkage groups, for example: [118][119][120].…”

Stress-Tolerant Feedstocks for Sustainable Bioenergy Production on Marginal Land

“…Even though plant height and total biomass decreased under heat stress [249], a climate modeling paper shows that Panicum virgatum yields could increase under warmer climate scenarios (3 to 8°C), due to extended growing season and limited cold stress [211].…”

Emerging tools, concepts and ideas to track the modulator genes underlying plant drought adaptive traits: An overview

“…55 Transcriptome based gene prospecting approach is gaining momentum these days. [56][57] Proteome and metabolome analyses in different plant species contributed to a better understanding of molecular mechanisms that are involved under drought. [58][59][60] There are several omics data repositories which are publically available as listed in Table 1, which can hasten our access to data generated for multilevel analysis for a comprehensive understanding of the experimental scenario.…”