Integrated Transcriptomic and Epigenomic Analysis in Switchgrass

Epigenetic mechanisms regulate several physiological processes including plant growth, development, signaling, and abiotic and biotic stress-responses. Switchgrass is a dedicated herbaceous bioenergy feedstock for cellulosic ethanol production. The main objective in switchgrass research has been the improvement of biomass yield, production and its lignocellulosic conversion into biofuel. Until now, genomic and transcriptomic approaches have been utilized in addressing yield-related traits but integrated epigenomic and transcriptomic analyses have not been undertaken, especially the role of chromatin modifications on gene expression. Genome-wide transcriptome profiling revealed 6,619 and 5,369 genes that were differentially expressed between upland (AP13) and lowland (VS16) ecotypes, respectively. Gene ontology and KEGG pathway annotations identified genes involved in phenylpropanoid, C4 and photorespiration-related pathways, and drought-, heat-, and salinity- tolerance, transporters in stress, and disease-resistance in the two ecotypes. The majority of pathways identified here belonged to metabolic processes. To understand chromatin modification at the whole-genome level, we used chromatin immunoprecipitation sequencing (ChIP-Seq) to analyze DNA binding of H3K9_me2 and H4K12_ac marks in both genotypes. More than 70% of the sequenced reads were mapped to reference genome (AP13). The number of histone-DNA binding regions was higher in H4K12_ac than H4K9_me2 in both genotypes. About 60% of the peaks were related to genic region (upstream, 5’-UTR, exon, intron, 3’-UTR and downstream) in both modifications. This integrated analysis will aid not only in developing reference epigenomes and transcriptomes in switchgrass but also in understanding the interplay between epigenomic modulators and gene expression in plant stress responses.