Abstract
BackgroundThe functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments.ResultHere, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3′ ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates.ConclusionsThese analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.
Highlights
The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement
Since cis-regulatory elements (CREs) are difficult to identify by sequence alone, various Encyclopedia of DNA Elements (ENCODE)-like projects have emerged with the goal of annotating the non-coding, functional genome in a given species by generating spatiotemporal maps of chromatin accessibility, transcription factors (TFs) occupancy, protein and DNA modifications, and gene expression [5, 6]
Mapping accessible chromatin in early development of maize inflorescences To determine the regulatory landscape of the maize genome during early inflorescence development, we generated genome-wide, tissue-specific maps of accessible chromatin from immature tassels and ears
Summary
The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Growth and development of all organisms depends on coordinated regulation of gene expression in time and space In order for this to occur, chromatin conformation must be remodeled so that specific sequences in the DNA are accessible to regulatory transcription factors (TFs) [1]. It was reported that approximately 1% of the genome was accessible based on differential MNase sensitivity in nuclei from young seedlings, yet this fraction explained 40% of the heritable variation [17] These results indicated that, as in animal systems, functional polymorphisms are enriched in accessible regions of plant genomes, which has significant implications for advancing genome-assisted breeding. Variations on these developmental programs at the molecular level result in distinct structural features at maturity that directly affect yield potential, e.g., outgrowth of branches in the tassel and development of kernel rows on the ear [32, 33]
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