A Genome-Wide Regulatory Framework Identifies Maize Pericarp Color1 Controlled Genes

Pericarp Color1 ( P1 ) encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize ( Zea mays ) silks and red phlobaphene pigments in pericarps and other floral tissues, which makes P1 an important visual marker. Using genome-wide expression analyses (RNA sequencing) in pericarps and silks of plants with contrasting P1 alleles combined with chromatin immunoprecipitation coupled with high-throughput sequencing, we show here that the regulatory functions of P1 are much broader than the activation of genes corresponding to enzymes in a branch of flavonoid biosynthesis. P1 modulates the expression of several thousand genes, and ∼1500 of them were identified as putative direct targets of P1 . Among them, we identified F2H1 , corresponding to a P450 enzyme that converts naringenin into 2-hydroxynaringenin, a key branch point in the P1 -controlled pathway and the first step in the formation of insecticidal C -glycosyl flavones. Unexpectedly, the binding of P1 to gene regulatory regions can result in both gene activation and repression. Our results indicate that P1 is the major regulator for a set of genes involved in flavonoid biosynthesis and a minor modulator of the expression of a much larger gene set that includes genes involved in primary metabolism and production of other specialized compounds.