CAREER: Genomic, cellular, and physiological effects of whole genome duplications on organismal energy production

该奖项全部或部分由《2021年美国救援计划法案》（公法117-2）资助。了解植物细胞如何产生能量的遗传基础是植物生物学的中心目标，特别是在作物改良努力的背景下。然而，基因与这些基因编码的能量相关性状之间的联系是复杂的，主要有两个原因：(1)能量相关基因分布在三个独立的细胞区室（细胞核、叶绿体和线粒体）；(2)所有植物在其进化史上都经历过一次或多次全基因组复制事件，其中核基因组已经加倍或更多。事实上，我们许多最重要的作物物种在细胞内都有两个以上的核基因组拷贝。这种“基因组冗余”如何影响能源生产在很大程度上是未知的；然而，核基因组拷贝数与线粒体和叶绿体之间的平衡似乎对植物的能量生产至关重要。我们将在新墨西哥理工学院（西班牙裔服务机构）雇用和培训一批不同的早期职业科学家，研究植物细胞如何维持这种平衡。大部分研究将在基于课程的研究经验的背景下进行，本科生和早期研究生将同时学习必要的生物技术，并有助于理解植物生物能量学。我们还将让高中生参与基因组学革命，分别在索科罗高中（Socorro， NM）和北太浩高中（Tahoe City， CA）现场对木酚油和雪花的基因组进行测序。每年夏天，一名高中实习生将参加NMT的植物基因组学研究。全基因组复制事件（WGDs）是植物多样化的主要动力，其中核基因组由于异源多倍体化或自多倍体化而加倍或更多。由于细胞质基因组与核基因组的复制（和遗传）是分开的，因此在WGD后，三个基因组区室之间的化学计量平衡（即细胞核化学计量）预计会受到干扰。最近的研究表明，在单子体和双子体中，细胞核化学计量在WGD后保持不变，这表明核基因组和细胞质基因组之间的基因剂量平衡是多倍体谱系形成和进化的重要组成部分。因此，我们假设，细胞核化学计量对确定细胞的叶绿体和线粒体含量至关重要，因此，细胞核化学计量的变化导致光合作用和呼吸性能的变化，并且细胞核化学计量的基因组结构响应核基因组大小和含量的变化。我们将首先在二倍体、多倍体和非整倍体环境中通过量化和测量细胞器、评估光合作用性能、比较细胞核和细胞质转录库来验证这些假设。我们还将在拟南芥基因组中进行关联测试，并通过分子敲除来确认这些关联，以解开细胞核化学计量学基础上复杂的基因组结构。作为这项研究的一部分，不同的研究人员联盟将有助于为未来旨在改善多倍体作物代谢功能的应用工作奠定基础，通过解决知识差距和增加21世纪农业改进努力所必需的人类基础设施。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 award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2).Understanding the genetic underpinnings of how plant cells produce energy represents a central goal in plant biology, especially in the context of crop improvement efforts. However, the connection between genes and the energy-related traits those genes encode is complicated for two primary reasons: (1) energy-related genes are spread across three separate cellular compartments (the nucleus, the chloroplasts, and the mitochondria), and (2) all plants have experienced one or more whole genome duplication events, in which the nuclear genome has been doubled or more, during their evolutionary history. Indeed, many of our most important crop species have more than two copies of their nuclear genome inside their cells. How this “genomic redundancy” affects energy production is largely unknown; however, the balance between nuclear genome copy number and the mitochondria and chloroplasts appears to be critical to plant energy production. We will employ and train a diverse group of early career scientists at New Mexico Tech (Hispanic Serving Institution), to investigate how plant cells maintain this balance. Much of the research will take place in the context of Course-based Research Experiences in which undergraduate and early-stage-graduate students will simultaneously learn the necessary biological techniques and contribute to the understanding of plant bioenergetics. We will also engage high school students in the genomics revolution by sequencing the genomes of creosote and snowflower live-and-in person at Socorro High School (Socorro, NM) and North Tahoe High School (Tahoe City, CA) respectively, and one high-school intern will participate in plant genomics research at NMT each summer.Whole genome duplication events (WGDs), in which the nuclear genome is doubled or more as a result of allopolyploidization or autopolyploidization, are a major force for plant diversification. Because the cytoplasmic genomes are separately replicated (and inherited) from the nuclear genome, the stoichiometric balance between the three genomic compartments (i.e., cytonuclear stoichiometry) is expected to be perturbed following WGD. Recent work indicates that cytonuclear stoichiometry is maintained following WGD in both monocots and eudicots, suggesting that gene dosage balance between the nuclear and cytoplasmic genomes represents an important component of polyploid lineage formation and evolution. We therefore hypothesize that cytonuclear stoichiometry is critical for establishing the cell’s chloroplast and mitochondrial content, such that variation in cytonuclear stoichiometry leads to variation in photosynthetic and respiratory performance and that the genomic architecture of cytonuclear stoichiometry is responsive to changes in nuclear genome size and content. We will test these hypotheses first in diploid, polyploid, and aneuploid contexts by quantifying and measuring organelles, evaluating photosynthetic performance, and comparing nuclear vs. cytoplasmic transcript pools of single cells. We will also perform association tests in the Arabidopsis thaliana genome and confirm those associations with molecular knockouts to disentangle the complex genomic architecture underlying cytonuclear stoichiometry. The diverse coalition of researchers employed as part of this research will be instrumental in setting the stage for future applied efforts aimed at improving metabolic function in polyploid crops, both by addressing knowledge gaps and by adding to the human infrastructure necessary for 21st century agricultural improvement efforts.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.