NSF Postdoctoral Fellowship in Biology FY 2021: Environmental influence and mechanisms underlying subgenome dominance in Camelina sativa

本行动资助2021财年美国国家科学基金会植物基因组生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。Jordan Brock博士的研究和培训计划的标题是“亚麻荠亚基因组优势的环境影响和机制”。该奖学金的主办机构是密歇根州立大学和博伊斯·汤普森研究所，赞助科学家是帕特里克·艾杰博士和安德鲁·纳尔逊博士。许多农业上重要的植物是杂交事件的产物，在杂交事件中，两个或多个亲本物种的基因组聚集在一起形成一个新物种（例如，油菜、棉花或小麦）。这些被称为多倍体的植物通常更能抵抗环境压力，因为它们每个基因都有多个拷贝（来自亲本亚基因组），为克服挑战提供了更大的工具箱。然而，人们对多倍体在多大程度上优先利用不同亲本来源的基因来克服环境挑战知之甚少。本项目将研究亲本亚基因组在多倍体生物燃料作物亚麻荠克服环境胁迫中的作用。具体来说，这项工作将解决温度在决定种子油生产亚基因组偏差中的作用。通过探究由每个亚基因组编码的潜在基因对环境决定的反应背后的机制，这项工作将为开发更具抗逆性的作物提供基因组理解和资源。该研究员将接受基因组学、表观基因组学和生物信息学方面的技术培训。除了指导和培训本科研究人员外，还将通过生物燃料教育模块在K-12学校开展植物生物学和基因组学的推广工作。本项目旨在利用基因组技术了解每个亚基因组在非生物胁迫（温度）调控中对亚麻荠籽油生产的相对贡献。Camelina是一种新兴的航空生物燃料作物，是两种亲本物种C. hispida和C.忽视的杂交和全基因组复制的产物。众所周知，亚麻荠籽油的质量和成分受温度等环境条件的影响很大。该项目将采用转录组和亚硫酸盐测序来了解亚基因组之间的表达水平如何随着温度胁迫而相互变化。将亚麻荠及其两个二倍体亲本种在不同的环境条件下一起生长，并在多个时间点提取发育中的种子。转录组和DNA甲基化文库将在不同的种子发育阶段和不同的环境中进行测序，以检查亚基因组特异性的贡献。一种假设是多倍体植物具有调节亚基因组表达的能力，因此最适应当前环境的亚基因组将得到更显著的表达。此外，DNA甲基化模式跨苜蓿亚基因组将被检查，以了解亚基因组表达水平优势背后的机制。本项目产生的数据将在同行评审的出版物中发表，转录组学和表观基因组学产生的数据将在国家生物技术信息中心的数据库中公开提供。所有其他数据，包括表型数据，将在Dryad中公开提供。该奖项反映了美国国家科学基金会的法定使命，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。

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2021. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Dr. Jordan Brock is "Environmental influence and mechanisms underlying subgenome dominance in Camelina sativa". The host institutions for the fellowship are Michigan State University and Boyce Thompson Institute and the sponsoring scientists are Dr. Patrick Edger and Dr. Andrew Nelson.Many agriculturally important plants are the product of hybridization events in which the genomes of two or more parental species come together to form a new species (e.g., canola, cotton, or wheat). These plants, known as polyploids, are often more resistant to environmental stress because they have multiple copies of each gene (from their parental subgenomes) providing a larger toolkit for overcoming challenges. However, little is known about the degree to which polyploids preferentially utilize genes of different parental origin to overcome environmental challenges. This project will address the role parental subgenomes play in overcoming environmental stresses in the polyploid biofuel crop, camelina. Specifically, this work will address the role of temperature in determining subgenome bias in seed oil production. Through interrogation of the mechanisms behind environmentally determined responses by the underlying genetics encoded by each subgenome, this work will provide the genomic understanding and resources for the development of more resilient crops. The fellow will receive technical training in genomics, epigenomics, and bioinformatics. Outreach in plant biology and genomics will be conducted in K-12 schools through a biofuel education module, in addition to the mentoring and training of undergraduate researchers.This project aims to use genomic techniques to understand the relative contribution of each subgenome in the regulation of abiotic stress (temperature) with regard to seed oil production in Camelina sativa. Camelina, an emerging aviation biofuel crop, is the product of a hybridization and whole-genome duplication between two parental species, C. hispida and C. neglecta. The quality and composition of camelina oil is known to be influenced greatly by environmental conditions such as temperature. This project will employ transcriptome and bisulfite sequencing to understand how expression-levels among subgenomes change relative to each other as a consequence of temperature stress. Camelina sativa and its two diploid parental species will be grown together in varying environmental conditions and developing seeds will be extracted at multiple timepoints. Transcriptome and DNA methylation libraries will be sequenced across distinct developmental stages of the seed, and in varying environments, to examine subgenome-specific contributions. One hypothesis is that polyploid plants have the ability to regulate subgenome expression such that the subgenome most adapted to the current environment will be more dominantly expressed. Additionally, DNA methylation patterns across C. sativa subgenomes will be examined to understand the mechanisms behind subgenome expression level dominance. Data generated in this project will be presented in peer-reviewed publications, and transcriptomic and epigenomic data generated will be made publicly available in National Center for Biotechnology Information databases. All other data, including phenotypic data, will be made publicly available in Dryad.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.