NSF Postdoctoral Fellowship in Biology: Interplay of Ploidy and the Distribution of Fitness Effects in Brassica

NSF 生物学博士后奖学金：倍性的相互作用与芸苔属适应性效应的分布

• 批准号: 2209085
• 负责人: Justin Conover
• 金额: $ 21.6万
• 依托单位: Conover, Justin L
• 依托单位国家: 美国
• 项目类别: Fellowship Award
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-03-01 至 2026-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2209085&HistoricalAwards=false
• 关键词: NSF; Postdoctoral; Fellowship; Biology; Interplay

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2022. 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. Justin Conover is “Interplay of Ploidy and the Distribution of Fitness Effects in Brassica”. The host institution for the fellowship is the University of Arizona and the sponsoring scientists are Drs. Michael Barker and Ryan Gutenkunst.The domestication of wild plants to create agricultural crops resulted in many changes in their genomes. Understanding those changes can deepen our understanding of agricultural history and potentially guide future crop improvements. DNA mutations can affect an individual’s evolutionary fitness (ability to survive and reproduce), with consequences ranging from lethality, to having no effect, to being highly beneficial. However, our understanding of mutation fitness effects in crops is incomplete, largely because many crops have more than two complete sets of chromosomes, which complicates genomic analyses and may affect how mutations change fitness. This project will develop new approaches to understand the fitness effects of mutations in plants and apply them to multiple economically important Brassica crops, including canola, broccoli, cauliflower, and turnips. The tools developed and insights gained will be applicable to many other crops including cotton, wheat, peanuts, and quinoa. Broader impacts from this project will increase the participation of students from historically underrepresented groups in STEM, including Alaskan Natives and Native Americans, as well as members of the LGBTQ+ community, through paid research opportunities and free public workshops to prepare application materials for graduate schools and external fellowships. Training objectives include obtaining expertise in the application of computational and statistical methods to population-level genomic data and the analysis of gene expression data.The distribution of fitness effects (DFE) of new mutations is a fundamental concept in population genetics that is important for understanding and predicting how natural selection operates in populations. Considerable attention has been given to understand how properties of the DFE can differ between populations in animal model systems, but DFE research has been relatively neglected in plants. Although many crop systems have undergone recent and recurrent whole genome duplication (polyploidy) events, often accompanied by interspecific hybridization, the ways in which shifts in ploidy levels affect the DFE in plants are poorly understood. This project uses allopolyploid Brassica napus, and its diploid progenitors B. rapa and B. oleracea to characterize how ancient and recent polyploidy events influences the DFE of a population and to model correlations in the DFE between the subgenomes of a single allopolyploid population. The work will be achieved primarily through the use and development of the Python package dadi (Diffusion Approximation for Demographic Inference) and publicly available transcriptomic and whole-genome resequencing data. All data, scripts, and methodological advances will be made available in public repositories, and all software will be open-source and freely available.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.

这项行动为2022财年的NSF植物基因组博士后生物学研究奖学金提供资金。该研究金支持研究员在东道实验室的研究和培训计划，研究员还提出了扩大生物学参与的计划。Justin科诺菲尔博士的研究和培训计划的标题是“芸苔属植物倍性的相互作用和健身效应的分布”。该奖学金的主办机构是亚利桑那大学，赞助科学家是Michael Barker博士和Ryan Gutenkunst博士。野生植物的驯化创造农作物导致了基因组的许多变化。了解这些变化可以加深我们对农业历史的理解，并可能指导未来的作物改良。DNA突变可以影响个体的进化适应性（生存和繁殖的能力），其后果从致命到没有影响，再到非常有益。然而，我们对作物突变适应性影响的理解是不完整的，主要是因为许多作物有两套以上的完整染色体，这使基因组分析复杂化，并可能影响突变如何改变适应性。该项目将开发新的方法来了解植物突变的适应性效应，并将其应用于多种经济上重要的芸苔属作物，包括油菜、西兰花、花椰菜和芜菁。开发的工具和获得的见解将适用于许多其他作物，包括棉花，小麦，花生和藜麦。该项目的更广泛影响将增加来自STEM历史上代表性不足的群体的学生的参与，包括阿拉斯加原住民和美洲原住民，以及LGBTQ+社区的成员，通过付费研究机会和免费的公共研讨会来准备研究生院和外部奖学金的申请材料。培训目标包括获得计算和统计方法应用于群体水平基因组数据和基因表达数据分析的专业知识。新突变的适应度效应分布（DFE）是群体遗传学中的一个基本概念，对于理解和预测自然选择如何在群体中运作非常重要。在动物模型系统中，研究者们对DFE的特性在种群间的差异给予了相当大的关注，但在植物中的DFE研究相对被忽视。虽然许多作物系统经历了最近和经常性的全基因组重复（多倍体）事件，往往伴随着种间杂交，倍性水平的变化影响植物中的DFE的方式知之甚少。本研究利用异源多倍体甘蓝型油菜及其二倍体祖细胞B。rapa和B.甘蓝来表征古代和近代的多倍体事件如何影响群体的DFE，并对单个异源多倍体群体的亚基因组之间的DFE中的相关性建模。这项工作将主要通过使用和开发Python包dadi（人口统计推断的扩散近似）和公开可用的转录组和全基因组重测序数据来实现。所有的数据、脚本和方法学进展都将在公共资源库中提供，所有的软件都将是开源和免费的。该奖项反映了NSF的法定使命，并被认为值得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来支持。