P0017
Transcriptome Analysis of Two Switchgrass Ecotypes: AP13 (lowland) and VS16 (upland)

Elizabeth Fiedler , Delaware State University, Dover, DE
Vasudevan Ayyappan , Molecular Genetics & Epigenomics Laboratory, Delaware State University, Dover, DE
Venkateswara R. Sripathi , Center for Molecular Biology, Alabama A&M University, Normal, AL
Malay C. Saha , The Samuel Roberts Noble Foundation, Ardmore, OK
Jyothi Thimmapuram , Bioinformatics Core, Purdue University, West Lafayette, IL
Ketaki Bhide , Purdue University, West Lafayette, IN
Venu (Kal) Kalavacharla , Molecular Genetics & Epigenomics Laboratory, Delaware State University, Dover, DE
Switchgrass is a C4 perennial grass used as a biofuel crop because of its high carbon storage potential, biomass conversion ratio, diverse propagative abilities, and inherent tolerance to several biotic and abiotic stresses. Lowland ecotypes are typically favorable for their high biomass yield as well as heat and drought tolerance. In some areas, upland ecotypes are favored for their adaptability to cold conditions. Switchgrass ecotypes, AP13 (lowland) and VS16 (upland), were grown in greenhouse and leaf samples were collected. Total RNA was isolated from these samples, cDNA was synthesized, and libraries were constructed and sequenced on Illumina HiSeq2500. Sequences were analyzed using TopHat and Cufflinks to identify differential gene expression between the contrasting ecotypes. This study identified 5,369 and 6,620 significantly (>2-fold) expressed genes in AP13 and VS16, respectively. The transcripts were annotated and differentially expressed genes were classified based on their function and physiological processes. Over 100 transcription factors were differentially expressed between the two ecotypes. KEGG pathway analysis identified pathways related to biomass production in these ecotypes, including C4 photosynthesis, photorespiration, and phenylpropanoid pathways. Several genes involved in stress responses related to drought, heat, flooding, salinity, and pathogen defense were identified. RNA binding proteins, Mei2-like, pumilio, and RRM domain containing proteins were also found and are implicated in post-transcriptional gene regulation. Differentially expressed genes from each category were selected and validated with RT-PCR and qRT-PCR. This study provides comprehensive transcript profiling in the switchgrass ecotypes and will aid in exploring genetic potential for future crop improvement efforts.
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