Progress in the science of genomics is no longer limited by the technologies that obtain genomic DNA sequence, but rather by the ability to interpret this information and uncover biologically relevant features of the genome. In addition, DNA sequence is only one component of the information content of the genome. Additional information - called epigenetic information - is encoded partly by the protein-containing matrix called chromatin in which the DNA is packaged. Specific modifications to the histone proteins, which make up the bulk of chromatin, are closely associated with the characteristics of the genes to which they are affixed. The objective of this project is to evaluate novel approaches to facilitate sequence analysis of gene-rich regions in plants with complex genomes, identify chromatin landmarks useful for genome annotation, and identify polymorphic sequences most useful for genetic map construction, utilizing a wild apple species as a reference. The project is expected to help uncover how epigenetic information is linked to gene activity, add accuracy to annotation efforts, and uncover cryptic and previously unanticipated features of the plant genome.
The broader impacts of this project include its potential as a training opportunity in the biological sciences for students and scientists at multiple levels, including postdoctoral, graduate, undergraduate, and K-12. The project will provide numerous opportunities to link researchers interested in genomics, gene expression, plant physiology, development, biotechnology, plant breeding and bioinformatics. The studies will establish a wild apple species as a simple model for genomics and genetics of the agriculturally important M. domestica, thus enabling tractable functional genomics, rapid forward and reversed genetic analyses, and comparative genomics in apple. In addition, the project will provide the foundation for identification of alleles governing interesting traits seen in wild apples that could be deployed in new cultivars optimized for low-input, high-volume 21st-century production methods. Finally, as epigenetic mechanisms are well conserved across multicellular organisms and have been implicated in human disease and stem cell dynamics, the project has obvious impacts for advancement of human medicine. The project will generate resources needed by the plant research community, including genic sequence across much of the euchromatic gene space, an exhaustive transcriptome (EST) database, and detailed gene expression atlas of development. These results will be made available to the public through the Genomic Database for the Rosaceae (GDR; www.bioinfo.wsu.edu/gdr/), a dedicated project website, and from the National Center for Biotechnology Information (NCBI).
Progress in the science of genetics is no longer limited by our ability to read and decode DNA sequence. Instead, we are challenged by our ability to interpret genomes in terms of biologically significant information - which ultimately programs the growth and development of all higher life forms including humans and plants. Much of this information is encoded within the proteins that package and organize the long strands of DNA - called chromatin. Specific types and arrangements of chromatin can either repress or enhance the activity of the genes that are packaged. In this project, we identified the major gene-repressive and gene-activating types of chromatin, and used a technique to map these chromatin types within the genome of a tree called Oregon Crabapple (Malus fusca). This is a small and fast-growing plant that is easy to work with in the laboratory, and can be used as a model for apple and other tree species that are important for horticulture, agriculture and forestry. We also carried out a high-definition analysis of gene activity throughout development in this plant, to determine when and where specific genes are active or repressed, and how this activity relates to chromatin features. This was one of the most extensive analyses of gene activity that has been done to date, in any organism. The results of these studies will allow scientists to more easily determine the significance of certain chromatin features in plant genomes. These results will also lead to methods to increase efficiency of genome sequencing, by allowing sequencing targeted to specific chromatin features. Because chromatin and DNA is very similar between plants, animals and humans, much of these results can be applied to animal agriculture and human biology. This project integrated computer science and bioinformatics with laboratory and field studies, and provided educational and training opportunities for postdocs, graduate students, undergraduates, and high-school students. The project also served as the catalyst to create an ongoing model program that fosters scientific research collaboration between faculty, undergraduates and high school students. This program, called CoHoRT (College-High School Research Teams) connects juniors from urban high schools with undergraduates from similar backgrounds in cutting edge-research projects directed by a faculty member. The project is expected to enhance the education of the students, strengthen applications for admission to programs of higher study, and ultimately create a diverse STEM workforce that is more cognizant of challenges facing all members of society.
