NSF Postdoctoral Fellowship in Biology FY 2019: Quantifying the Impact of Transposable Elements on Maize Fitness and Adaptation

这一行动为NSF国家植物基因组计划2019财年生物学博士后研究奖学金提供了资金。该奖学金支持在东道主实验室为该研究员制定的研究和培训计划，该研究员还提出了扩大生物学参与度的计划。米歇尔·斯蒂泽的这项研究和培训计划的标题是“量化转座元素对玉米适应性和适应性的影响”。该奖学金的主办机构是康奈尔大学，赞助科学家是塞德里克·费肖特博士和爱德华·S·巴克勒博士。转座元素是可以跳到基因组中新位置的DNA片段。与可靠地代代相传的基因不同，转座元件可以在整个基因组中的新位置移动并产生新的自身副本。它们最初是在玉米中发现的，现在已知存在于整个生命树的基因组中。它们在植物基因组中特别活跃，占水稻基因组DNA的40%，占玉米和小麦基因组DNA的85%以上。尽管已经假设转座元件会产生对适应压力环境有价值的突变，但这还没有得到全面的测试。该项目测试了新的转座对玉米适应性的影响，并开发了植物基因组中可转座元件注释的计算资源，可能对非植物基因组产生影响。更广泛的影响包括举办以使用统计编程语言R为重点的讲习班。这些讲习班将为生物学本科生量身定做，重点是增加在STEM中任职人数不足的学生的参与。培训目标包括获得植物表型、计算和分子技术方面的专业知识，以及向不同受众交流编码和生物信息学技术的经验。大多数植物基因组是由转座子组成的，但人们对转座子的运动如何影响植物的适合性和表型知之甚少。以玉米为模式系统，该项目将直接调查转座元素对植物适合性和对选择的反应的影响。具体目标是：1)开发软件来检测和注释已测序的参考基因组中的转座元素；2)对玉米的作图群体进行表型，该群体的转座元素的拷贝数不同，以测试拷贝数是否影响产量和其他与适应性相关的性状；以及3)通过化学去甲基化在全基因组范围内激活转座元素，以测试新的插入是否会产生在适应非生物胁迫期间选择的突变。所有项目成果将通过各种公共储存库供更广泛的研究界使用。所有产生的数据、脚本和软件将通过GitHub、FigShare(https://figshare.com)，MaizeGDB和/或NCBI-SRA)公开提供。本项目产生的种质将保存在玉米遗传合作储备中心。关键词：转座基因、玉米遗传学、适应性、基因组注释该奖项反映了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。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2019. 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 Michelle Stitzer is "Quantifying the impact of transposable elements on maize fitness and adaptation" The host institution for the fellowship is Cornell University and the sponsoring scientists are Drs. Cedric Feschotte and Edward S. Buckler.Transposable elements are pieces of DNA that can jump to new positions in genomes. Unlike genes which are reliably inherited from generation to generation, transposable elements can move and generate new copies of themselves at novel positions throughout the genome. Originally discovered in maize, they are now known to exist in genomes across the tree of life. They are particularly active in plant genomes, making up 40% of the DNA in the rice genome and over 85% of the DNA in the maize and wheat genomes. Although transposable elements have been hypothesized to produce mutations valuable for adaptation to stressful environments, this has not been comprehensively tested. This project tests the impact of new transposition on maize adaptation and develops computational resources for transposable element annotation in plant genomes with possible implications for non-plant genomes. Broader impacts include the development of workshops focused on the use of statistical programming language R. These workshops will be tailored to undergraduate biology students with a focus on increasing participation from students underrepresented in STEM. Training objectives include obtaining expertise in plant phenotyping, computational, and molecular techniques as well as experience in communicating coding and bioinformatic techniques to diverse audiences. The majority of plant genomes are comprised of transposable elements, but little is known about how their movement impacts plant fitness and phenotypes. Using maize as a model system, the project will directly investigate the impact of transposable elements on plant fitness and response to selection. Specific objectives are to: 1) develop software to detect and annotate transposable elements in sequenced reference genomes; 2) phenotype a mapping population of maize that varies in copy number of a transposable element to test whether copy number impacts yield and other fitness-related traits; and, 3) activate transposable elements genome-wide by chemical demethylation to test whether novel insertions generate mutations selected for during adaptation to abiotic stress. All project outcomes will be made accessible for use by the broader research community through various public repositories. All data, scripts, and software produced will be publicly available through GitHub, Figshare (https://figshare.com), MaizeGDB, and/or NCBI-SRA. Germplasm generated in this project will be deposited in the Maize Genetics Cooperation Stock Center. Keywords: transposable elements, maize genetics, adaptation, genome annotationThis 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.