The initiative is building on the extensive research already accomplished on the American chestnut by the American Chestnut Foundation and others as a model system for how biotechnology can potentially protect trees, and restore species devastated by disease. The near-term goal is to safely and effectively develop an American chestnut that is resistant to the chestnut blight and root rot, and which can be safely restored to our forests. While working to help restore the American chestnut as the test tree, the program will discover new approaches to enhance the health and vitality of other trees, forests, and forest ecosystems. Download the FHI Science Plan Overview.

Science Pathways

Biotech Trees

Society needs healthier forests and the ecosystem services they provide. Biotechnology is a powerful tool that under appropriate conditions, may be applied to forestry. Developing biotech trees to combat invasive threats is critical to improve the future of our forests and the benefits society derives from them.


The goal for the genome resources and tools project is to provide a high-quality reference sequence for the Castanea mollissima (Chinese Chestnut) genome, with which to identify genes for resistance to Cryphonectria parasitica. In addition, the broad impact of this project will be to demonstrate the power of genomics to address the increasing forest health and ecosystem restoration issues that we face now and in the future.

The genome resources and tools project builds upon the results of the NSF-sponsored Genomic Tool Development for the Fagaceae project ( and brings together experts and cutting-edge facilities in genomics and bioinformatics from Penn State University and the Clemson University Genomics Institute. Our approach to develop a high quality reference genome sequence for Chinese chestnut (Castanea mollissima) cv Vanuxem is through deep "next generation" DNA sequencing technologies, following a two year time line. The Vanuxem cultivar was chosen for the reference genome due to its key role in The American Chestnut Foundation’s breeding program ( and the NSF Fagaceae Tools project. The reference genome will be assembled de novo from 454 sequence data, corrected and extended with Illumina sequence data, and pseudo-chromosomes built by integration of the physical and genetic maps for chestnut. Bioinformatic analyses will then target genome regions associated with blight resistance. Resistance genes will be identified by transcript mapping and/or by gene-finding algorithms. To facilitate the discovery of resistance genes, additional genomes will be produced by “resequencing” including the Mahogany variety of Chinese chestnut, a blight-sensitive American chestnut and blight-resistant hybrids. The genes discovered will be provided to the FHI transformation project for functional studies. SNPs spanning the genome will also be discovered and put into use by the FHI genetic technologies group to accelerate breeding. Overview of FHI's Genomic Resources and Tools

Germplasm & Breeding

The goal of the Germplasm, Breeding, and Testing (GBT) Team is to provide a bridge between the other two Biological Sciences Teams (Transgenics and Genomics) by supplying them with the materials and information needed to develop an efficient transgenics pipeline within the context of improving forest health through species/ecosystem restoration. The GBT Team is working with American chestnut breeding programs to provide materials to the Transgenics Team for use in developing and identifying productive somatic embryogenic (SE) lines for transformation experiments and field testing. The GBT Team is verifying and more precisely defining the genetic/genomic location of genes conferring resistance to Cryphonectria blight in the ‘Mahogany’ Chinese line of interspecies hybrid materials and providing this information to the Genomics Team for use in candidate gene identification and selection. In addition, this information is being provided to the breeders and used to develop efficient marker-assisted selection technologies for chestnut breeding. DNA sequences containing candidate genes are provided by the Genomics Team to the Transgenics Team to be introduced into various SE lines. Transformed and non-transformed SE lines are provided back to the GBT Team for field testing. In this manner the three Biological Sciences Teams are highly interwoven providing a system with feedback loops that can be used over time to develop and test increasingly advanced materials.

Transformation & Clonal Testing

  1. Test first-generation transgenic events and gene constructs currently in the transformation pipeline,
  2. Establish scalable pipeline for embryogenic culture initiation and somatic seedling regeneration, capturing existing American chestnut (AC) and AC hybrid germplasm,
  3. Integrate transformation capability into pipeline, propagate multiple transgenic AC events harboring blight resistance candidate genes (CGs) from multiple sources,
  4. Develop modular vector resources for rapid integration of selectable markers, regulatory elements, and multi-gene constructs,
  5. Establish field sites for germplasm production and standardize disease screening protocols,
  6. Develop an accurate, early blight resistance screening protocol to pre-screen transgenic trees before entering field trials.

The over arching goal is to establish embryogenic systems and capacity for high throughput initiation, capture, regeneration, testing, and cryopreservation of conventionally bred and transgenic American chestnut (AC) germplasm. First generation transgenic AC lines will be propagated for near term deployment, at replicated field sites, for development and standardization of early and conventional screening protocols. Concurrently, we will coordinate germplasm collection with the Germplasm Team to initiate embryogenic cultures and screen selections for embryogenesis, clonal propagation potential, and propagule quality. We will integrate high efficiency Agrobacterium mediated transformation, co transformation, and liquid selection systems for scalable production of individual genotypes. One, or a few, “workhorse lines” are being developed for rapid vector integration that will enable molecular characterization of vector properties and blight resistance candidate gene constructs. We will initiate development of environmental impact protocols that will guide deployment strategies for transgenic germplasm in forest restoration efforts.