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

该奖项的全部或部分资金来自《2021年美国救援计划法案》(公法117-2)。了解植物细胞如何产生能量的遗传基础代表着植物生物学的一个中心目标，特别是在作物改良努力的背景下。然而，基因和这些基因编码的与能量相关的特征之间的联系是复杂的，主要有两个原因：(1)与能量相关的基因分布在三个独立的细胞间隔(核、叶绿体和线粒体)中；(2)在所有植物的进化历史中，都经历了一个或多个全基因组复制事件，其中核基因组翻了一番或更多。事实上，我们许多最重要的作物物种的细胞内都有两个以上的核基因组副本。这种“基因组冗余”如何影响能量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能量产生至关重要。我们将雇佣和培训新墨西哥理工学院(西班牙裔服务机构)的一批早期职业科学家，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，在这些经验中，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(新墨西哥州索科罗)和北塔霍高中(加州塔霍市)对杂酚油和雪花同居的基因组进行测序，每年夏天将有一名高中实习生参加NMT的植物基因组研究。全基因组复制事件(WGDS)是由于异源多倍化或同源多倍化导致核基因组翻一番或更多的事件，是植物多样性的主要力量。由于细胞质基因组是从核基因组单独复制(和遗传)的，因此WGD后三个基因组区段之间的化学计量平衡(即细胞核化学计量)可能会受到干扰。最近的工作表明，在WGD后，单子叶植物和真子叶植物的细胞核化学计量比都保持不变，这表明核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，细胞核化学计量学对于确定细胞的叶绿体和线粒体含量是至关重要的，这样，细胞核化学计量学的变化就会导致光合作用和呼吸性能的变化，并且细胞核化学计量学的基因组结构对核基因组大小和含量的变化做出反应。我们将首先在二倍体、多倍体和非整倍体的背景下测试这些假设，方法是量化和测量细胞器，评估光合作用性能，并比较单细胞的核转录库和细胞质转录库。我们还将在拟南芥基因组中进行关联测试，并确认这些与分子敲除的关联，以解开支撑细胞核化学计量学的复杂基因组结构。作为这项研究的一部分，受雇的不同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努力奠定基础，这既是通过解决知识差距，也是通过增加21世纪农业改良工作所需的人类基础设施。这一奖项反映了NSF的法定使命，并通过使用基金会的智力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.