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

本行动资助2023财年美国国家科学基金会植物基因组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。Charity Goeckeritz的研究和培训计划的题目是“用比较基因组学的方法来理解蔷薇科无融合性的遗传调控”。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。由于减数分裂的过程，种子通常含有父母双方DNA的混合物。植物育种家利用减数分裂创造新的植物品种，但有时一个珍贵的选择必须保持和广泛分布，需要大量的时间和资源。无融合是植物繁殖的一种自然偏差，最常发生在玫瑰，雏菊和草科，导致母植物的无性系种子。因此，它提供了一种保存优良植物品种的手段；这也增加了果实落地的可能性。尽管如此，无融合的遗传基础仍然难以捉摸，因此它被称为“植物育种的圣杯”。“对无融合生殖的研究仅限于速生植物，这在很大程度上排除了玫瑰科（蔷薇科）的植物，比如苹果和黑莓。”然而，随着DNA测序技术的进步，对蔷薇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。就更广泛的影响而言，除了其植物育种意义外，这项工作还提供了一个机会，向公众传达自然植物多样性与相关物种的重要性。此外，这个项目的最先进的科学技术将教授给未来的科学家，重点是传统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。无融合或无性种子生产是禾科、菊科和蔷薇科常见的一种趋同性状。几十年来，它一直吸引着研究人员，因为它可以提高生殖适应性并保持优良的作物遗传。因此，无融合在物种适应和作物改良方面具有广泛的意义。这个项目的重点是蔷薇科无杂交的遗传学，这是一个由于长世代时间而历史上研究不足的领域。比较基因组学将用于鉴定与无融合相关的DNA序列及其进化轨迹。首先，将为不同繁殖模式的苹果和红莓物种制作阶段性基因组。其次，亚基因组和/或整个单聚类将使用k-mer聚类和系统发育评估分组。这将通过揭示无融合性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测序来探索两种生殖途径之间的差异。项目成果包括作物近缘的基因组资源和对设计蔷薇科无杂交育种策略至关重要的信息。该项目的数据将在玫瑰科基因组数据库（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络（www.ars-grin.gov）中提供。这项奖励反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行了评估，认为值得支持。

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.