The regulatory landscape of early maize inflorescence development

The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements and regulatory DNA revealed through chromatin accessibility maps can be harnessed for manipulating gene expression to subtle phenotypic outputs that enhance productivity in specific environments. Here, we present a genome-wide view of accessible chromatin and nucleosome occupancy at a very early stage in the development of both pollen- and grain-bearing inflorescences of the important cereal crop maize (Zea mays), using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion. Results showed that in these largely undifferentiated tissues, approximately 1.5-4 percent of the genome is accessible, with the majority of MNase hypersensitive sites marking proximal promoters but also 3' flanks of maize genes. This approach mapped regulatory elements to footprint-level resolution, and through integration of complementary transcriptome and transcription factor occupancy data, we annotated regulatory factors such as combinatorial motifs and long non-coding RNAs that potentially contribute to organogenesis in maize inflorescence development, including tissue-specific regulation between male and female structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity, revealed new SNP-trait associations in known regulators of inflorescence development. These analyses provide a first look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential. Overall design: As detailed below, we analyzed 2 different tissue types, maize tassel and ear primordia. Nucleosome bound DNA from these primordia were digested with low (light digest) and high (heavy digest) concentration of micrococcal nuclease enzyme followed by high-throughput sequencing to investigate the chromatin landscape. The differential between light and heavy digests and the different size classes of sequenced reads were used to call nucleosomal and transcription factor footprints. Two biological replicates were used per tissue per micrococcal nuclease enzyme concentration.