Development of Reference Epigenomes and Transcriptomes in Switchgrass

Epigenetic mechanisms are one of the most important regulatory processes in plant development and physiological response to environmental signals. Majority of the plant epigenetic studies have been conducted in Arabidopsis, rice and maize and there is a need to expand these studies to other plant species. Switchgrass (Panicum virgatum L.) is an economically important, warm-season, and widely adapted C4 perennial grass. Switchgrass shows tremendous promise as a candidate crop for the U.S. biofuel industry. High biomass yield potential under marginal environments, sequestering large amounts of atmospheric carbon, and sustainable productivity across a wide geographical range, made switchgrass, a dedicated herbaceous bio-energy crop for cellulosic biofuel production. Until now, most research in switchgrass has been focused on the improvement of biomass yield, and yield related traits but epigenomics research, especially in the area of histone-DNA interactions as related to stress have not been studied. In this study we have developed a protocol for switchgrass chromatin immunoprecipation (ChIP) followed by next generation sequencing (ChIP-seq) in two switchgrass genotypes, AP13 and VS16, for understanding global binding locations of two histone marks, H3K9me2 and H4K12ac, and the relationship of histone binding location and gene expression. We found 34,739 significantly differentially expressed genes between AP13 and VS16 with FDR value of <0.05. Among them number of up-regulated genes in AP13 and VS16 were 15,462 and 19,275 respectively. These reference epigenomes and transcriptomes will be used for understanding the effects of abiotic and biotic stresses on the epigenome as well to discover genotype-specific epigenomic variation.