Major alterations in transcript profiles between C3-C4 and C4 photosynthesis of an amphibious species Eleocharis baldwinii

Engineering C-4 photosynthetic metabolism into C-3 crops is regarded as a major strategy to increase crop productivity, and clarification of the evolutionary processes of C-4 photosynthesis can help the better use of this strategy. Here, Eleocharis baldwinii, a species in which C-4 photosynthesis can be induced from a C-3 -C-4 state under either environmental or ABA treatments, was used to identify the major transcriptional modifications during the process from C-3 -C-4 to C-4. The transcriptomic comparison suggested that in addition to the major differences in C-4 core pathway, the pathways of glycolysis, citrate acid metabolism and protein synthesis were dramatically modified during the inducement of C-4 photosynthetic states. Transcripts of many transporters, including not only metabolite transporters but also ion transporters, were dramatically increased in C-4 photosynthetic state. Many candidate regulatory genes with unidentified functions were differentially expressed in C-3 -C-4 and C-4 photosynthetic states. Finally, it was indicated that ABA, auxin signaling and DNA methylation play critical roles in the regulation of C-4 photosynthesis. In summary, by studying the different photosynthetic states of the same species, this work provides the major transcriptional differences between C-3 -C-4 and C-4 photosynthesis, and many of the transcriptional differences are potentially related to C-4 development and therefore are the potential targets for reverse genetics studies.