Plants are frequently subjected to fluctuating and extreme abiotic environments and must adapt rapidly. Epigenetics provides a layer of responsiveness that operates at the interface of genome and environment. Research in the Madzima Lab incorporates molecular genetics, genomics and genome editing to elucidate how epigenetic mechanisms facilitate plant responses to abiotic stress and development in Zea mays (maize) and other agriculturally important crop plants.
We study the RNA-dependent DNA methylation (RdDM) pathway, a plant-specific epigenetic pathway that functions to direct changes in DNA (cytosine) methylation, chromatin structure and gene expression at target loci (reviewed by Matzke and Mosher, 2014). In maize, the MEDIATOR OF PARAMUTATION 1 (MOP1) protein is required for the progression of the RdDM pathway. The mop1-1 mutation has served as a valuable resource as it disrupts the majority of the RdDM epigenetic pathway and allows us to probe our research questions.
Thus far, the Madzima lab has 3 main projects/objectives. Together, these projects will allow us to genetically dissect the fundamental mechanisms of epigenetic regulation in response to abiotic stress, that can be manipulated in plants to develop climate resistant crops.
The phytohormone abscisic acid (ABA) serves as a critical regulator of plant responses to specific abiotic stress stimuli. In a transcriptomic analysis using plants defective in epigenetic regulation (mop1-1), we previously identified synergistic targets of epigenetic and ABA-mediated regulatory networks in the maize genome (Vendramin et al., 2020; Madzima et al. 2021). These synergistic targets are enriched for genes involved in plant growth and development, including development of inflorescences that impact seed yield and warrant further investigation. Several of these genes encode transcription factors (TFs) predicted to function in a hierarchical cascading gene regulatory network. Ongoing working included identification and functional validation of putative regulatory genes that mediate the synergy between epigenetic and ABA regulatory pathways.
We are interested in understanding how stress-induced epigenetic regulatory mechanisms have evolved in other crop plants. The Poaceae (grass) family includes several agronomically important crop plants that are divergent in their photosynthetic mechanisms (C3 vs. C4), as well as responses and tolerance to abiotic stress (e.g., drought and high temperatures). Members of this family are also divergent in their genome sizes and transposable element (TE) content. By comparing epigenetic regulatory activities in specific members of the Poaceae family, we aim to extrapolate the impact of environmentally-induced gene regulation associated with cis-variation and proximity of different TE families to regulated genes.
Several genes with predicted roles in plant growth, development and reproduction are uniquely differentially expressed in mop1-1 mutants relative to their wildtype siblings. Consistently, plants experiencing a loss of MOP1-mediated RdDM activity have pleiotropic developmental defects that negatively affect seed yield. We aim to probe the molecular mechanisms of a MOP1-mediated RdDM pathway on maize inflorescence development. We are currently using genetic mutants of candidate genes to probe their role in maize inflorescence and seed development.