A combination of RNA-Seq and ChIP-Seq reveals multiple roles of P1 in pericarp development and metabolic pathways

KENGO MOROHASHI; ALPER YILMAZ; LUCILLE POURCEL; MARÍA ISABEL CASAS; JULIA EMILIANI; MA LORENA FALCONE FERREYRA; MICHAEL MCMULLEN; PAULA CASATI; ERICH GROTEWOLD

St. Charles, Illinois, USA

Congreso; 53rd Annual Maize Genetics Conference; 2011

The maize pericarp is the outside layer of the seed coat, and it acts as the first barrier to insects and pathogens. It is also important for the quality of canned corn and popcorn as a moisture barrier. Depending on the genetic background, the pericarp can accumulate the phlobaphene pigments, derived from the polymerization of the 3-deoxyflavonoids and controlled by P1 (Pericarp Color1), corresponding to R2R3-MYB transcription factor. P1 also controls the accumulation of insecticidal C-glycosyl flavones in silks. While the metabolic steps resulting in the formation of a common precursor for the formation of the phlobaphenes and C-glycosyl flavones are known, most of the later steps in the respective pathways remain unidentified. To date, only the A1 gene, encoding dihydroflavonol reductase (DFR), has been confirmed as an immediate direct target of P1. In order to establish the overall regulatory function of the P1 gene, we performed a genome-wide analysis by a combination of RNA-Seq and ChIP-Seq in P1-rr, specifying red pericarp and red cob glume color and P1-ww, which harbors a null P1 allele lacking phlobaphene pigments. We successfully obtained short read sequence tags from mRNA and ChIP DNA extracted from pericarp cells of P1-rr and P1-ww at two different developmental stages, 15 and 25 DAP. The computational analysis of RNA-Seq and ChIP-Seq data revealed that P1 particularly plays a role in the flavonoid pathway, and to a lesser extent in the phenylpropanoid pathway. It also suggested that P1 could be part of other biological processes. This is the first report of the comprehensive analysis that integrated the information of gene expression changes and binding locations of a tissue specific transcription factor in maize. This project was funded by grant NSF DBI-0701405.