Progress is 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 is encoded partly by the proteinaceous matrix called in which the DNA is packaged - called chromatin.  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 chromatin structure is linked to gene activity, add accuracy to annotation efforts, and uncover cryptic and previously unanticipated features of plant genomes.

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 (Malus fusca) 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 chromatin-related 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.

National Science Foundation
Division of Biological Infrastructure
Plant Genome Research Program

Exploiting Chromatin Landmarks to Characterize Complex Plant Genomes

Project DBI-0922447
Steve van Nocker, PI vannocke@msu.edu

Project Studies:

Genomic DNA sequence:

Transcriptional (RNA-seq) data:

Chromatin-tagged sequence (ChIP-seq):