Identification of Rice Secondary Cell Wall Associated Regulators via Genome-scale Network Analysis

Grasses cover approximately 20% of terrestrial land and provide 50% of human calories. When dried, secondary cell walls (SCW) are the bulk of grass biomass. Despite the difference between grass and dicot SCW components and patterning, relatively little is known about grass SCW regulators. To map the grass SCW regulatory cascade, we developed a generalized linear model-based scoring system to build the Rice Combined mutual Ranked (RCR) network with data from three publicly available rice coexpression and functional genome-scale networks, namely, ROAD, PlaNet and RiceNet. The RCR network covers ~90% of the genome and to our knowledge, it is the most complete rice network developed so far. We evaluated the network quality with biological process GO terms using Receiver-Operating Characteristic curves assessed by the area under the curve (AUC). The AUC of the RCR network is greater than the original networks, suggesting it is also a high-quality network. Next, we extracted a cell wall network with rice homologs of known Arabidopsis cell wall-related transcription factors, lignin biosynthesis genes and grass-diverged cell wall crosslinking enzymes (acyltransferases). The cell wall network identifies 37 unstudied putative cell wall-associated transcription factors in addition to recalling 85% of expected interactions between transcription factors and cell wall synthesis genes. Our transient gene expression assays in rice protoplasts validate 53% (8 out of 15) of the tested transcription factors. This study facilitates understanding of regulatory mechanisms among species to enable the control of SCW biosynthesis in grasses for improved fuel, feed, and fiber production.