Zea mays subsp. mays cultivar:B73 Epigenomics

Every cellular process mediated through nuclear DNA must contend with chromatin. We use an MNase hypersensitivity assay to discover open chromatin regions in the maize reference genome. We show that maize MNase hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots. We also demonstrate that they focus biased gene conversion at their flanks. Finally, we show that MNase HS regions – comprising less than 1% of the genome – consistently explain approximately 40% of the heritable phenotypic variance in diverse quantitative traits, with the remainder of the variance primarily explained by the coding sequence. Altogether, our results imply that less than 3% of the maize genome may explain most of the variation in both molecular and organismal-level phenotypes, greatly narrowing the scope of the functional genome.