Development and Use of Tools for Switchgrass Functional Genomics

Switchgrass is a perennial C4 grass with potential to become a major bioenergy crop.  To help realize this potential, a set of RNA-based resources were developed.  Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16.  Over 11.5 million high-quality ESTs were generated with 454 sequencing technology and an additional 169,079 Sanger sequences were obtained from the 5’ and 3’ ends of 93,312 clones from normalized, full-length-enriched cDNA libraries.  AP13 and VS16 ESTs were assembled into 77,854 and 30,524 unique transcripts (unitranscripts), respectively, using the Newbler and PAVE programs.  Published Sanger-ESTs (544,225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128,058 unitranscripts, which were annotated for function.  An Affymetrix cDNA microarray chip (Pvi_cDNAa520831) containing 122,973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA).  The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data.  The PviGEA was used to identify representatives of all known genes in the phenylpropanoid-monolignol biosynthesis pathway.