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

研究-PGR：杂种和异源多倍体亚基因组优势的基因组学和表观基因组学

• 批准号: 2029959
• 负责人: Patrick Edger
• 金额: $ 260万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-11-01 至 2024-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2029959&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Genomics; Epigenomics; Subgenome

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.

许多作物物种是异源多倍体，由不同物种的杂交加上全基因组加倍形成，这早已被认为有助于重要农艺性状的出现。然而，在杂种和异源多倍体中，与其他“顺从”亚基因组相比，异源多倍体中的亲本亚基因组之一通常更显性地表达。这可能导致某些遗传途径以及最终的重要性状由单个亲本亚基因组显性控制。该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基础。鉴定表观遗传标记或其他基因组特征，表明显性表达的亚基因组，编码重要的目标性状，将大大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方面的跨学科培训。该项目还旨在扩大K-12学生的科学参与，跨越科学研究中代表性不足的群体，包括通过密歇根州立大学4-H儿童花园的活动。 最后，该项目将举办一个研讨会，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。使用比较基因组平台，包括二倍体祖先和多倍体物种基因组，结合转录组和多样化的表观基因组数据集，该项目旨在利用一套跨基因组的方法，和种内杂种以及自然形成的多倍体草莓。通过确定多个基因组和亚基因组中的调控区和转录因子（TF）结合位点，包括与非生物胁迫反应相关的TF结合基序，该项目将提供最全面的遗传和表观遗传变化的图片，发生在杂交和异源多倍体化和环境在塑造和确定亚基因组表达优势模式的潜在作用。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知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Chromosome painting reveals inter‐chromosomal rearrangements and evolution of subgenome D of wheat

染色体绘画揭示了小麦染色体间重排和 D 亚基因组的进化

• DOI: 10.1111/tpj.15926
• 发表时间: 2022
• 期刊: The Plant Journal
• 作者: Shi, Peiyao;Sun, Haojie;Liu, Guanqing;Zhang, Xu;Zhou, Jiawen;Song, Rongrong;Xiao, Jin;Yuan, Chunxia;Sun, Li;Wang, Zongkuan
• 通讯作者: Wang, Zongkuan

The power of chromosome-scale, haplotype-resolved genomes

染色体规模、单倍型解析基因组的力量

• DOI: 10.1016/j.molp.2022.02.010
• 发表时间: 2022
• 期刊: Molecular Plant
• 影响因子: 27.5
• 作者: Edger, Patrick P.

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

• DOI: 10.1101/814491
• 发表时间: 2019-10
• 期刊: The New Phytologist
• 作者: Kevin A. Bird;Chad Niederhuth;Shujun Ou;Malia A. Gehan;J. C. Pires;Zhiyong Xiong;R. VanBuren