RESEARCH-PGR: Deciphering the link between RNA directed DNA methylation and reproduction in Brassicaceae

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Seeds are the primary source of calories for humans and livestock, and thus one of the most critical aspects of agricultural productivity is seed development. Even small changes in seed development can have profound impacts on productivity with cascading repercussions through the entire food chain. This proposal addresses the role of DNA methylation, a chemical mark placed on DNA, in the development of seeds, particularly those marks that impact seed set, size, and viability. We have recently uncovered three mutations of a DNA methylation pathway in the important oil crop Brassica rapa. Each mutation has severe and specific defects in seed production. Using advanced DNA sequencing technologies, we will identify the genetic, molecular, and genomic consequences of these mutations. These findings will help understand the internal mechanisms that regulate seed development. This project will also provide training opportunities for multiple graduate and undergraduate students. This training will develop their expertise in cutting-edge techniques such as genome editing and high-throughput sequencing.This work builds on several key observations that link small-RNA directed DNA methylation (RdDM) with proper seed development, likely through establishment and maintenance of: 1) genomic imprinting (parent-of-origin bias in allele expression), and/or 2) genome balance (preferential expression from a dominant subgenome following whole genome duplication). This project will first explore the transcriptional and developmental consequences of RdDM in seed development by profiling small RNAs, transcriptomes, and epigenomes of RNA-directed DNA methylation mutants in Brassica rapa, each of which dramatically reduces seed set. In addition, we will investigate links between genomic imprinting and genome dominance in B. rapa. Finally, we will test the hypothesis that RdDM influences seed set by altering genomic imprinting and/or genome dominance by generating cognate mutations in other members of the Brassicaceae family. Results from this study will provide a better understanding of both imprinting and genome dominance that can be translated to closely related species in the family Brassicaceae, including the seed crop B. napus.