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NSF Postdoctoral Fellowship in Biology FY 2020: Genetic Determinants of Hybrid Decay in Backcross Populations of Teosinte with Maize

2020 财年 NSF 生物学博士后奖学金：类蜀黍与玉米回交群体中杂种衰变的遗传决定因素

基本信息

批准号：
2010908
负责人：
Manisha Munasinghe
金额：
$ 21.6万
依托单位：
Munasinghe, Manisha A
依托单位国家：
美国
项目类别：
Fellowship Award
财政年份：
2021
资助国家：
美国
起止时间：
2021-01-01 至 2023-12-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2010908&HistoricalAwards=false
关键词：
NSF Postdoctoral Fellowship Biology FY

项目摘要

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2018. 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 Manisha Munasinghe is "Genetic Determinants of Hybrid Decay in Backcross Populations of Teosinte with Maize". The host institution for the fellowship is the University of Minnesota and the sponsoring scientists are Drs. Yaniv Brandvain and Nathan Springer. Plant breeders seek to take advantage of useful genetic variants present in wild relatives of crop species. Genetic incompatibilities between species can work against this goal, which makes understanding how they emerge and persist in populations highly relevant. A unique incompatibility between the crop species maize and its wild relative the Mexican teosinte is thought to be triggered by the uncontrolled proliferation of repetitive DNA in hybrids. This project is designed to not only identify the specific genetic variants underlying this incompatibility but also to use this knowledge to expand evolutionary theory to better understand how these variants become established in populations. Training objectives for the Fellow include plant biology, computational biology, statistical genetics, and analytical modeling. Broader impacts include the development of two teaching modules in genetics and statistics for undergraduate students and providing mentoring and training through participation in the Carpentries (www.carpentries.org) computational training workshops. There is a longstanding interest in understanding the genomic basis of reproductive isolation as it can both inform how speciation occurs and the evolutionary forces occurring within lineages. The uncoupling of selfish repetitive DNA, such as transposable elements, and the molecular machinery that epigenetically silences their proliferation is a potential cause of hybrid incompatibility that has received comparatively little attention. This project explores an unusual case of hybrid incompatibility between the crop species maize and its wild relative Mexican teosinte thought to be caused by the uncoupling of repetitive DNA from the variants that halt their proliferation. No abnormal phenotype in the F1 hybrids, the persistence of the incompatibility despite recurrent backcrossing to maize, and epigenetic changes in hybrids distinguish this case from others. This project will characterize the genomic basis of this epistatic incompatibility, estimate its frequency in nature, and model its impacts on genome-wide patterns of introgression. Long-read, whole-genome sequencing will allow the fine-scale characterization of changes in repetitive DNA between the parental species and hybrids. Additional teosinte samples will be collected to perform population-level analyses to identify regions under selection, which will likely include repetitive DNA repressor systems. Finally, the consequence of uncoupling repetitive DNA from its repressor system will be modelled to characterize its effect on population divergence. All computer pipelines and codes will be shared publicly so other researchers may adapt these tools to their needs. Raw data/code will be released through public repositories, such as GitHub or NCBI. Processed datasets will be released through CyVerse Data Commons, Dryad, or DRUM (www.lib.umn.edu/datamanagement/drum). All processed data and any files that may be of interest to the broader community will be made publicly available through CyVerse or GitHub and will also be shared with MaizeGDB.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.

本行动资助NSF国家植物基因组计划2018年度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。Manisha Munasinghe的研究和培训计划的标题是“大刍草与玉米回交群体杂交衰变的遗传决定因素”。该奖学金的主办机构是明尼苏达大学，赞助科学家是dr。Yaniv Brandvain和Nathan b施普林格。植物育种家试图利用农作物野生近缘种中存在的有用遗传变异。物种之间的遗传不相容可能不利于这一目标，这使得了解它们如何在种群中出现并持续存在具有高度相关性。玉米和其野生亲缘种墨西哥大刍草之间独特的不亲和性被认为是由杂交品种中重复DNA的不受控制的增殖引发的。这个项目的目的不仅是确定这种不相容背后的特定遗传变异，而且要利用这些知识来扩展进化理论，以更好地理解这些变异是如何在种群中建立起来的。研究员的训练目标包括植物生物学、计算生物学、统计遗传学和分析建模。更广泛的影响包括为本科生开发遗传学和统计学两个教学模块，并通过参加Carpentries （www.carpentries.org）计算培训讲习班提供指导和培训。长期以来，人们一直对了解生殖隔离的基因组基础感兴趣，因为它既可以告诉物种形成是如何发生的，也可以告诉谱系内发生的进化力量。自私重复DNA的解偶联，如转座元件，以及表观遗传上使其增殖沉默的分子机制是杂交不相容的潜在原因，但很少受到关注。这个项目探索了一个不同寻常的情况，即玉米和它的野生亲戚墨西哥大刍草之间的杂交不亲和性，这种不亲和性被认为是由阻止它们增殖的变异的重复DNA的解耦引起的。在F1杂交种中没有异常表型，尽管与玉米反复回交，但不亲和性的持续存在，以及杂交种的表观遗传变化将这种情况与其他情况区分开来。该项目将描述这种上位性不相容的基因组基础，估计其在自然界中的频率，并模拟其对全基因组渗入模式的影响。长读全基因组测序将允许对亲本物种和杂交物种之间重复DNA的变化进行精细的表征。将收集更多的大刍草样本，进行种群水平的分析，以确定选择中的区域，其中可能包括重复的DNA抑制系统。最后，从其抑制系统中解耦重复DNA的后果将建模，以表征其对种群分化的影响。所有计算机管道和代码都将公开共享，以便其他研究人员可以根据自己的需要调整这些工具。原始数据/代码将通过公共存储库发布，如GitHub或NCBI。处理后的数据集将通过CyVerse Data Commons、Dryad或DRUM （www.lib.umn.edu/datamanagement/drum）发布。所有处理过的数据和任何可能对更广泛的社区感兴趣的文件将通过CyVerse或GitHub公开提供，也将与MaizeGDB共享。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。