Developmental Genetic Mechanisms of C(4) Syndrome Based on Transcriptome Analysis of C(3) Cotyledons and C(4) Assimilating Shoots in Haloxylon ammodendron

It is believed that transferring the C(4) engine into C(3) crops will greatly increase the yields of major C(3) crops. Many efforts have been made since the 1960s, but relatively little success has been achieved because C(4)plant traits, referred to collectively as C(4) syndrome, are very complex, and little is known about the genetic mechanisms involved. Unfortunately, there exists no ideal genetic model system to study C(4) syndrome. It was previously reported that the Haloxylon species have different photosynthetic pathways in different photosynthetic organs, cotyledons and assimilating shoots. Here, we took advantage of the developmental switch from the C(3) to the C(4) pathway to study the genetic mechanisms behind this natural transition. We compared the transcriptomes of cotyledons and assimilating shoots using mRNA-Seq to gain insight into the molecular and cellular events associated with C(4) syndrome. A total of 2959 differentially expressed genes [FDR≤0.001 and abs (|log(2)(Fold change)|≥1)] were identified, revealing that the transcriptomes of cotyledons and assimilating shoots are considerably different. We further identified a set of putative regulators of C(4) syndrome. This study expands our understanding of the development of C(4) syndrome and provides a new model system for future studies on the C(3)-to- C(4) switch mechanism.