NSF Award
2414478
The genomes of plants often vary substantially in their size and organization, even among individuals within the same species. An enduring mystery is how genomes can differ so dramatically and yet still produce functional organisms that are recognizable as a specific species. In this study, we will investigate genome diversity in corn (maize) to test a specific idea. Genomes are like strings that fold into loops. We suspect that the ends of the loops define active (or functional) regions of the genome, and that these regions remain stable among individuals. We also hypothesize that the size and content of the loops themselves is more variable, because they are a mechanism to sequester regions that are less important to genome function. To test this hypothesis, we will measure folding structures of 25 corn genomes and compare those structures across different individuals. We will measure folding by two methods, one that focuses on the entire genome and another that focuses on small stretches of DNA. By testing our hypotheses, we will gain insight into the enduring mystery of plant genome variability and generate basic knowledge about how plant genomes work. <br/><br/>This proposal focuses on measuring two types of genome variability among the parents of the maize Nested Association Mapping panel and two outgroup species (Sorghum bicolor and Setaria italica). The first type is DNA sequences that can form pre-miRNA-like stem-loops. These structures impact genome function when transcribed and when present in DNA; they are often the locus of small RNA production that with downstream epigenetic effects. The second type is chromatin folding into higher-order loops and domains. These domains may contribute to genome function by co-locating groups of expressed genes, thereby defining ‘transcription factories’. Despite the potential significance of both structure types, their variability within populations and the pace of their evolution remains poorly understood. Our goals are to catalog homology and variability of these structures within- and between-species, to assess which structures are conserved, to explore their epigenetic and functional contributions and, finally, to characterize the evolutionary forces that shape their underlying sequence variability. Since both structures have hypothesized roles in transcription and chromatin confirmation, we predict that they may colocalize in three-dimensional genome space. This project will also contribute to the training of project personnel and enhance the research experiences and retention of underrepresented and minority undergraduates. As part of the predoctoral research experience, they will learn bioinformatics and data analysis skills in the PIs research laboratories.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
