At ambient temperature (25–30 oC) and the prevailing atmospheric CO2 levels (380 ppm), installing the C4 photosynthetic machinery in a C3 plant would potentially drive away the photorespiratory process through a carbon concentrating mechanism (CCM), thereby preventing oxygenation reaction of Rubisco. Development of C4 rice is a global research priority, for enhanced water use efficiency (WUE) and yield. At optimal environment, the difference in the solar energy to biomass conversion between C3 and C4 plants is mainly due to photorespiration. So, photorespiratory bypasses are the potential alternatives than conversion to C4. Genetically transformed C3 model plants with photorespiratory bypass had demonstrated higher biomass (under same environmental conditions) than its wild type. Using a transcriptome approach, we report here the differential expression pattern for photorespiratory genes and chloroplastic pyruvate dehydrogenase (plPdc) gene between the leaves, peduncle, and the developing grain tissues in three rice genotypes. In addition to pyruvate, glycolate and glyoxylate also are the substrates for the plPdc gene product and hence a suitable candidate for photorespiratory bypass.