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.