P0757Comparison of DNA Methylation in AP13 and VS16 Switchgrass (Panicum virgatum) Using High-Throughput Sequencing
Mollee C Dworkin
,
Molecular Genetics & Epigenomics Laboratory, Delaware State University, Dover, DE
Shaojun Xie
,
Purdue University, West Lafayette, IN
Malay C. Saha
,
Noble Research Institute, Ardmore, OK
Jyothi Thimmapuram
,
Purdue University, West Lafayette, IN
Venu (Kal) Kalavacharla
,
Delaware State University, Dover, DE
Switchgrass (
Panicum virgatum) has been deemed as a target bioenergy crop by the United States Department of Energy, since the 1990s. Switchgrass has high biomass yield from low nutrient input, high water use efficiency, and broad adaptability. The two major ecotypes of switchgrass which are lowland (usually 2n = 4x = 36) and upland (usually 2n = 8x = 72). This study compares AP13 (lowland ecotype) and VS16 (upland ecotype), both of which are tetraploid. Reads were mapped to the unpublished genome, assembled from AP13 in 18 scaffolds (Phytozome V2.1). In these scaffolds 1,505.2 Mb of sequence has been localized, with another 184.3 Mb of sequence that is not localized (totaling~1,689.6 Mb).
Genome annotation and assembly provide resources for the breeding of biotic and abiotic stress-resistant/tolerant plants. Response to stresses is correlated with changes in gene expression, which is regulated by transcription factors and also epigenetic factors. Transposable elements (TEs) play an important role in the evolution of plants and adaptation to stressful environments. TEs are often found to be heavily methylated in heterochromatic regions.
Genome-wide methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) and whole genome bisulfite-sequencing (BS-Seq) was performed to compare methylation levels between the two genotypes. MeDIP-Seq surveys overall differences between the genomes and BS-Seq gives specific methylation statuses of individual cytosines.
