Co-PI: Sridhar Hannenhalli, University of Maryland Co-PI: Chris Dardick, Appalachian Fruit Research Laboratory, USDA-ARS Co-PI: Ann Callahan, Appalachian Fruit Research Laboratory, USDA-ARS
Fruits that are so enjoyed by people are also especially adapted for plant seed dispersal. Even closely related plants display different types of fleshy fruits that accomplish dispersal through variation in color, shape, size, texture and other traits. A major question for plant biologists and fruit crop scientists is how these diverse fruit types evolved and what factors control their development. If scientists could explain the molecular basis of different fruit types, new breeding tools could be used to increase the value of fruit crops and basic research could be advanced. The Rose family (Rosaceae) is an excellent example of how fruits have been selected and adapted to different types of dispersal. Members of the family, including the familiar strawberries, apples, and roses, all have unique fruits and floral structures from which the fruits are derived. This project investigates how these different fruits develop at the molecular level. Using comparative genomic and bioinformatics methods, the research will identify shared and unique genes that control the pattern of fruit development among five representatives of the Rose family: strawberries, peach, plum, apple and raspberry. Computational methods will be used to identify regulatory gene networks that explain how and when the diverse fruits form. High school teachers will be brought into the research program during the summer to study fruit science and computational data analysis, and curricula will be developed for use in the high school classroom. By integrating teachers into the research, the next generation of students will be impacted broadly and will gain hands-on exposure to genomics and bioinformatics.
The project investigates the molecular genetic mechanisms that underlie the phenotypic diversity of fleshy fruits in the Rosaceae. By leveraging the evolutionary conservation of genes within the Rosaceae genome, the power of comparative genomics will be used to identify key genes and mechanisms of fleshy fruit development. The recently published Rosaceae genome sequences (apple, strawberry, peach, raspberry and plum) provide an unprecedented opportunity to investigate this fundamental biological question. First, detail morphological and histological changes during floral and early stage fruit development will be characterized for the chosen Rosaceae species. This knowledge will guide sample collection for RNA-sequencing methods immediately before and after fertilization in specific floral tissues. Innovative bioinformatic tools and strategies will be developed to identify toolkit genes and regulatory gene networks, whose spatial or temporal shifts of expression may alter fleshy fruit programs in different species. Functional tests including RNAi, CRISPR, and tissue-specific ectopic expression will be carried out to test predicted toolkit genes using the established transformation systems in strawberry, FasTrack plum, and apple. The ultimate goal is to identify causal relationships between changes of toolkit gene expression and evolution of distinct fleshy fruit types. The research activities will be integrated with several educational and outreach programs including training of students and postdoctoral researchers in genomics and informatics, bioinformatics workshops for high school teachers from rural West Virginia and predominantly minority-serving schools of Prince Georges County of Maryland, and outreach to the public about Genetically Modified Organisms and fruit genomics. All sequence data will be made available through the public NCBI database and through the community database for the Rosaceae.
