Rice genome-scale network integration reveals transcriptional regulators of grass cell wall synthesis

Grasses have evolved distinct cell wall composition and patterning
relative to dicotyledonous plants. However, despite the importance of this
plant family, transcriptional regulation of its cell wall biosynthesis is
poorly understood. To identify grass cell wall-associated transcription
factors, we constructed the Rice Combined mutual Ranked Network (RCRN).
The RCRN covers >90% of annotated rice (Oryza sativa) genes, is
high quality, and includes most grass-specific cell wall genes, such as
mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases.
Comparing the RCRN and an equivalent Arabidopsis network
suggests that grass orthologs of most genetically verified eudicot cell
wall regulators also control this process in grasses, but some vary
significantly in network connectivity between these divergent species.
Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal
that OsMYB61a activates a grass-specific acyltransferase promoter, which
confirms network predictions and supports grass-specific cell wall
synthesis genes being incorporated into conserved regulatory circuits. In
addition, 10 of 15 tested transcription factors, including six
novel wall-associated regulators (WAP1, WACH1, WAHL1, WADH1,
OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts
when transiently expressed. The results highlight the quality of the RCRN
for examining rice biology, provide insight into the evolution of cell
wall regulation, and identify network nodes and edges that are possible
leads for improving cell wall composition.