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

许多作物物种是异源多倍体，由不同物种杂交和全基因组加倍形成，这早已被认为是导致重要农艺性状出现的原因。然而，在杂交种和异源多倍体中，异源多倍体中的一个亲本亚基因组通常比另一个‘顺从’亚基因组(S)更具优势地表达。这可能导致某些遗传途径，最终是重要的特征，由单个亲代亚基因组主导控制。这个项目的一个主要目标是了解亚基因组表达优势的遗传和表观遗传学基础。表观遗传标记或其他基因组特征的识别表明了编码重要目标性状的主要表达的亚基因组，将极大地减少研究和育种多倍体作物的挑战。在培训和推广方面，该项目将为高中生、本科生、研究生和博士后研究人员提供植物遗传学、基因组学和系统生物学的跨学科培训。该项目还旨在扩大K-12学生的科学参与，包括通过在密歇根州立大学4-H儿童花园的活动，扩大在科学研究中代表性不足的群体。最后，该项目将主办一个研讨会，向更广泛的研究社区的不同科学家教授各种分子细胞遗传学技术。该项目使用由二倍体前体和多倍体物种基因组组成的比较基因组平台，结合转录组和多样化的表观基因组数据库，旨在通过一组种间和种内杂交以及自然建立的多倍体草莓，揭示在亚基因组显性的早期阶段发生的表观基因组和转录体变化。通过确定多个基因组和亚基因组中的调节区和转录因子(TF)结合部位，包括与非生物胁迫反应相关的转录因子结合基序，该项目将提供最全面的图景，以了解杂交和异源多倍化后发生的遗传和表观遗传变化，以及环境在形成和确定亚基因组表达优势模式中的潜在作用。所有方法和数据集将通过出版物和长期存储库公开提供。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.