Investigating Gene Expression and DNA Methylation Patterns Following Genome Duplication in Maize

Most crop plants are diploid (2n), meaning their genome contains two copies of each chromosome. Maize is no exception; however, it evolved from a tetraploid (4n) ancestor. Maize’s progression to a diploid state caused many gene losses and rearrangements, vastly altering its chromatin structure and genetic landscape. Understanding how polyploidy causes restructuring of the genome can elucidate maize’s evolutionary history and contribute to agricultural breeding programs. The effects of genome duplication can be studied through the analysis of gene expression and DNA methylation data. Diploid maize can become a tetraploid via the application of nitrous oxide during fertilization, which inhibits the first zygotic division of a fertilized egg cell. We used gene expression and DNA methylation data from diploids and induced autotetraploids to investigate changes in chromatin structure in B73 and Oh43 lines of maize that have undergone genome duplication. Through analyzing gene expression data and DNA methylation data from zygotene anther tissue, we were able to investigate these changes. We conducted a differential expression analysis in order to understand differences in gene expression between the diploid and tetraploid. This was followed by a gene set enrichment analysis, which identified the functions of the differentially expressed genes. We analyzed the DNA methylation data by studying genome-wide methylation patterns and identifying the locations of differentially methylated cytosines in tetraploids relative to their diploid counterparts. Ultimately, we found that genome duplication results in genome-wide changes in the rate of DNA methylation and that there are no common gene functions enriched among B73 and Oh43 tetraploids. These findings suggest genome duplication alters the methylome of maize, and that dosage effects, rather than relative gene expression differences may be the primary cause of the phenotypic differences commonly observed between diploids and tetraploids.

This summer I had the opportunity to pursue my interest in science through an internship in the Pawlowski lab at Cornell University. Over the past ten weeks I’ve gained invaluable experience organizing, analyzing, and interpreting real genomic data in a professional research environment. Additionally, I have learned firsthand about the exciting diversity of research in plant science through the weekly seminars organized by the Boyce Thompson Institute Research Experience for Undergraduates program. The program’s graduate studies panel, along with my interactions with many engaging faculty members and graduate students at Cornell, has stoked my enthusiasm for research, and helped me develop a more informed plan for continuing my education and developing a career in scientific research. I’m grateful to Quinn Johnson, Wojtek Pawlowski, Robert Bukowski, and Minghui Wang for their guidance and direction over the course of the program.