RESEARCH-PGR: Genomics and Epigenomics of Subgenome Dominance in Hybrids and Allopolyploids

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Many crop species are allopolyploids, formed by the hybridization of different species coupled with whole genome doubling, which has long been known to contribute to the emergence of important agronomic traits. However, one of the parental subgenomes in an allopolyploid is often more dominantly expressed compared to the other 'submissive' subgenome(s) in both hybrids and allopolyploids. This can result in certain genetic pathways, and ultimately important traits, being dominantly controlled by a single parental subgenome. A major goal of this project is to understand the genetic and epigenetic basis of subgenome expression dominance. The identification of epigenetic marks or other genomic features that indicate the dominantly expressed subgenome, which encodes for important target traits, would greatly reduce the challenge of researching and breeding polyploid crops. With respect to training and outreach, the project will provide interdisciplinary training in plant genetics, genomics, and systems biology, to high school, undergraduate, and graduate students, and postdoctoral researchers. This project also aims to broaden scientific participation of K-12 students, spanning under-represented groups in science research, including through activities at the Michigan State University 4-H Children’s Garden. Finally, the project will host a workshop that will teach various molecular cytogenetic techniques to diverse scientists in the broader research community.Using a comparative genomic platform, consisting of diploid progenitor and polyploid species genomes, combined with transcriptome and a diverse epigenomic dataset, this project aims to uncover the epigenomic and transcriptomic changes that occur during the earliest stages of subgenome dominance using a set of inter-and intra-specific hybrids and in naturally established polyploid strawberry. By identifying regulatory regions and transcription factor (TF) binding sites in multiple genomes and subgenomes, including TF binding motifs associated with abiotic stress response, this project will provide the most comprehensive picture of the genetic and epigenetic changes that occur following hybridization and allopolyploidization and the potential role of the environment in shaping and determining subgenome expression dominance patterns. All methods and datasets will be made publicly available through publications and through long-term repositories.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.