Drought tolerance is one of the most remarkable agronomic traits of switchgrass (Panicum virgatum). This study was undertaken to quantify the expression of the drought-induced leaf and root proteomes in switchgrass. Drought treatment was performed using a “sandwich” drought system that was developed to simulate the drought condition under field. Leaf tissues were harvested when the soil water tension reached 50 centibar. The top three leaves were used for protein extraction. Leaf protein extracts was treated using ProteoMiner technology to enrich the low-abundance proteins. Protein samples were digested with trypsin, and peptides were labeled with isobaric tags for relative and absolute quantitation (iTRAQ) and analyzed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) to identify the drought induced proteins. A total of 4,474 proteins were quantified in the crude leaf protein extracts (CLE) compared to 3,707 proteins in those after ProteoMiner treatment (PMT). 1,206 proteins were unique to the PMT samples. Thus, the use of the depletion process together with the crude leaf protein extracts is able to increase the number of proteins quantified in proteomics experiments. Approximately 5% of the quantified proteins showed significant differences between the control and drought-treated groups. Root tip and root elongation zone proteins were extracted from the switchgrass treated by severe drought (SDT), one-day re-watering (D1W) and three-days re-watering (D3W). For root tissues collection, root tip and root elongation was cut 1 cm from the distal end of root apex and root tip separately. Root protein samples were digested with trypsin, and peptides were labeled with tandem mass tags (TMT) and analyzed by nano-LC-MS/MS to identify the proteins induced under different levels of drought conditions. A total of 10,018 and 9,731 proteins were separately quantified from root tips and root elongation proteomes. In each of these root protein samples, more than 60% of the quantified proteins were up-regulated, except the D1W treated root elongation sample in which 88% were down-regulated proteins. The drought treatment and recover phases altered the abundance of proteins involved in different molecular functional pathways. These proteins may play important role in enabling switchgrass plants to be more tolerant of drought conditions
