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.

这项行动为2023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。该奖学金的研究和培训计划的标题慈善Goeckeritz是“比较基因组学方法来了解蔷薇科无融合生殖的遗传调控”。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。种子通常含有双亲DNA的混合物，这是由于一个称为“减数分裂”的过程。植物育种者利用减数分裂创造新的植物品种，但有时必须保持珍贵的选择并广泛分布，需要大量的时间和资源。无融合生殖是植物繁殖过程中的一种自然变异，最常发生在蔷薇、雏菊和禾本科植物中，其结果是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方法;它也增加了结果的可能性。尽管如此，无融合生殖的遗传基础仍然难以捉摸，使其获得了“植物育种的圣杯”的绰号。无融合生殖的研究一直保留在快速生长的植物，这在很大程度上排除了玫瑰科（蔷薇科）的植物，如苹果和黑莓。然而，随着DNA测序技术的进步，蔷薇科植物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确定控制这种现象的DNA序列。关于更广泛的影响，除了其植物育种意义外，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，该项目的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，是禾本科，菊科和蔷薇科家族经常表现出的趋同性状。几十年来，它一直吸引着研究人员，因为它可以增加生殖健康并保持优良作物遗传。因此，无融合生殖对物种适应和作物改良具有广泛的意义。该项目的重点是蔷薇科无融合生殖的遗传学，这是一个由于世代时间长而历史上研究不足的领域。比较基因组学将用于确定与无融合生殖相关的DNA序列的进化轨迹。首先，将为不同繁殖方式的苹果属和悬钩子属物种制作分相基因组。其次，将使用k-mer聚类对亚基因组和/或整个单倍体进行分组，并进行遗传学评估。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测序探索两种生殖途径之间的差异。项目成果包括作物近缘种的基因组资源和设计蔷薇科无融合生殖育种策略的关键信息。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基因库（www.ncbi.nlm.nih.gov/genbank）和美国农业部种质资源信息网（www.ars-grin.gov）中提供。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。