Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass.
Transcriptomes of two switchgrass genotypes representing the upland and lowland ecotypes will be key tools in switchgrass genome annotation and biotic and abiotic stress functional genomics. Switchgrass (Panicum virgatum L.) is an important bioenergy feedstock for cellulosic ethanol production. We report genome-wide transcriptome profiling of two contrasting tetraploid switchgrass genotypes, VS16 and AP13, representing the upland and lowland ecotypes, respectively. A total of 268 million Illumina short reads (50 nt) were generated, of which, 133 million were obtained in AP13 and the rest 135 million in VS16. More than 90% of these reads were mapped to the switchgrass reference genome (V1.1). We identified 6619 and 5369 differentially expressed genes in VS16 and AP13, respectively. Gene ontology and KEGG pathway analysis identified key genes that regulate important pathways including C4 photosynthesis, photorespiration and phenylpropanoid metabolism. A series of genes (33) involved in photosynthetic pathway were up-regulated in AP13 but only two genes showed higher expression in VS16. We identified three dicarboxylate transporter homologs that were highly expressed in AP13. Additionally, genes that mediate drought, heat, and salinity tolerance were also identified. Vesicular transport proteins, syntaxin and signal recognition particles were seen to be up-regulated in VS16. Analyses of selected genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, membrane transporters, heat, drought and salinity stress responses confirmed significant variation in the relative expression reflected in RNA-Seq data between VS16 and AP13 genotypes. The phenylpropanoid pathway genes identified here are potential targets for biofuel conversion.
Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA.
Vasudevan
V
Ayyappan
Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA.
Malay C
MC
Saha
Bioinformatics Core, Purdue University, West Lafayette, IN, USA.
Jyothi
J
Thimmapuram
Plant Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL, USA.
Venkateswara R
VR
Sripathi
Bioinformatics Core, Purdue University, West Lafayette, IN, USA.
Ketaki P
KP
Bhide
Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA.
Elizabeth
E
Fiedler
Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA.
Rita K
RK
Hayford
Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA. vkalavacharla@desu.edu.|Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE, USA. vkalavacharla@desu.edu.
Venu Kal
VK
Kalavacharla
D015536:Down-Regulation / Q000235:genetics; D060146:Ecotype; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005838:Genotype; D008897:Panicum / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics
Bioenergy; Lowland; Switchgrass; Transcriptome; Upland