NSF Postdoctoral Fellowship in Biology: A Comparative Genomics Approach to Understand the Genetic Regulation of Apomixis in Rosaceae

NSF 生物学博士后奖学金：了解蔷薇科无融合生殖遗传调控的比较基因组学方法

• 批准号: 2305693
• 负责人: Charity Goeckeritz
• 金额: $ 24.9万
• 依托单位: Goeckeritz, Charity Z
• 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: 2023-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2305693&HistoricalAwards=false
• 关键词: NSF; Postdoctoral; Fellowship; Biology; Comparative

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2023. 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 Charity Goeckeritz is ‘A Comparative Genomics Approach to Understand the Genetic Regulation of Apomixis in Rosaceae’. The host institution for the fellowship is the HudsonAlpha Institute for Biotechnology and the sponsoring scientist is Dr. Alex Harkess.Seeds usually contain a mixture of both parents’ DNA due to a process called ‘meiosis.’ Plant breeders take advantage of meiosis to create new plant varieties, but sometimes a prized selection must be maintained and widely distributed, requiring extensive time and resources. Apomixis is a natural deviation of plant reproduction occurring most often in the rose, daisy, and grass families that results in clonal seed of the mother plant. Therefore, it provides a means of preserving elite plant varieties; it also increases the probability of fruit set. Still, the genetic basis of apomixis remains elusive, earning it the moniker ‘the Holy Grail of plant breeding.’ The study of apomixis has been reserved for fast-growing plants, which largely excludes plants in the rose family (Rosaceae) like apples and blackberries. However, with access to recent technological advances in DNA sequencing, the study of apomixis in Rosaceae is within reach. Comparing genomes of species with and without the capacity for apomixis will help identify the DNA sequences controlling this phenomenon. With respect to broader impacts, apart from its plant breeding significance, this work provides an opportunity to communicate the significance of natural plant diversity with relatable species to the general public. Moreover, state-of-the-art scientific techniques for this project will be taught to future scientists, focusing on students at historically black colleges and universities. Training objectives include obtaining expertise in cutting-edge functional genomics tools and computational methods.Apomixis, or asexual seed production, is a convergent trait frequently exhibited by the Poaceae, Asteraceae, and Rosaceae families. It has captivated researchers for decades because it can increase reproductive fitness and maintain elite crop genetics. Thus, apomixis has broad implications for species adaptation and crop improvement. This project focuses on the genetics of apomixis in Rosaceae, an area historically understudied due to long generational times. Comparative genomics will be used to identify the DNA sequences associated with apomixis with respect to their evolutionary trajectory. First, phased genomes will be produced for Malus and Rubus species differing in their mode of reproduction. Second, subgenomes and/or entire haplomes will be grouped using k-mer clustering and phylogenetically assessed. This will guide genomic comparisons by revealing any convergent inheritance patterns of apomixis. Lastly, differences between the two reproductive pathways will be explored through single-nucleus RNA and ATAC sequencing. Project deliverables include genomic resources for crop relatives and information crucial for designing apomictic breeding strategies in the Rosaceae. Data for the project will be available in the Genomic Database for Rosaceae (www.rosaceae.org), the National Center for Biotechnology Information’s GenBank (www.ncbi.nlm.nih.gov/genbank), and the United States’ Department of Agriculture Germplasm Resources Information Network (www.ars-grin.gov).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.

这一行动为2023财年NSF植物基因组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。Charity Goeckeritz这一奖学金的研究和培训计划的标题是“一种了解蔷薇科无融合生殖遗传规律的比较基因组学方法”。该奖学金的主办机构是哈德逊·阿尔法生物技术研究所，赞助科学家是亚历克斯·哈克斯博士。由于一种被称为“减数分裂”的过程，种子通常含有父母双方的DNA。植物育种者利用减数分裂创造新的植物品种，但有时必须保持宝贵的选择并广泛分布，这需要大量的时间和资源。无融合生殖是一种植物繁殖的自然偏差，最常发生在玫瑰、雏菊和禾本科植物中，导致母体植物的克隆种子。因此，它提供了一种保存优良植物品种的手段，也增加了坐果的概率。尽管如此，无融合生殖的遗传基础仍然难以捉摸，因此被称为植物育种的圣杯。对无融合生殖的研究一直被保留在快速生长的植物上，这在很大程度上排除了玫瑰科(蔷薇科)植物，如苹果和黑莓。然而，随着最近DNA测序技术的进步，玫瑰科无融合生殖的研究已经触手可及。比较具有和不具有无融合生殖能力的物种的基因组将有助于识别控制这种现象的DNA序列。至于更广泛的影响，除了植物育种的意义外，这项工作还提供了一个机会，向公众宣传自然植物多样性与相关物种的重要性。此外，该项目最先进的科学技术将教授给未来的科学家，重点是历史上黑人学院和大学的学生。培训目标包括获得尖端功能基因组学工具和计算方法的专业知识。无融合生殖，或无性种子生产，是Poaceae、Asteraceae和Rosaceae家族经常表现出的一种趋同特征。几十年来，它一直吸引着研究人员，因为它可以增加生殖适应性并保持精英作物遗传学。因此，无融合生殖对物种适应和作物改良具有广泛的意义。本项目主要研究蔷薇科植物无融合生殖的遗传学，由于世代时间较长，这一领域历来未得到充分研究。比较基因组学将被用来确定与无融合生殖相关的DNA序列的进化轨迹。首先，将为繁殖模式不同的苹果和悬钩子物种产生阶段性基因组。其次，亚基因组和/或整个单倍体将使用k-mer聚类法进行分组并进行系统发育评估。这将通过揭示无融合生殖的任何趋同遗传模式来指导基因组比较。最后，将通过单核RNA和ATAC测序来探索这两条生殖途径之间的差异。可交付的项目包括作物近亲的基因组资源和设计蔷薇科无融合生殖育种战略的关键信息。该项目的数据将在蔷薇科基因组数据库(www.rosaceae.org)、国家生物技术信息中心的GenBank(www.ncbi.nlm.nih.gov/genBank)和美国农业部种质资源信息网(www.ars-grin.gov)中获得。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。