A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis

C4 photosynthesis is used by only three percent of all flowering plants, but explains a quarter of global primary production, including some of the worlds' most important cereals and bioenergy grasses. Recent advances in our understanding of C4 development can be attributed to the application of comparative transcriptomics approaches that has been fueled by high throughput sequencing. Global surveys of gene expression conducted between different developmental stages or on phylogenetically closely related C3 and C4 species are providing new insights into C4 function, development and evolution. Importantly, through co-expression analysis and comparative genomics, these studies help define novel candidate genes that transcend traditional genetic screens. In this review, we briefly summarize the major findings from recent transcriptomic studies, compare and contrast these studies to summarize emerging consensus, and suggest new approaches to exploit the data. Finally, we suggest using Setaria viridis as a model system to relieve a major bottleneck in genetic studies of C4 photosynthesis, and discuss the challenges and new opportunities for future comparative transcriptomic studies.