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

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.