Applying Genomic Resources to Restoration of an Iconic Forest Tree, the American Chestnut

For over thirty years, scientists and private citizens have worked together to restore the American chestnut (Castanea dentata), a foundational forest species in eastern North America that was eliminated as a canopy tree in the first half of the twentieth century. Genomic resources have been established for American chestnut and Chinese chestnut (C. mollissima), a major source of genetic resistance to chestnut blight (Cryphonectria parasitica). Genomic resources, including a draft reference genome of C. mollissima, resequencing of additional chestnut species, genetic maps, and a physical map, are poised for immediate translation into the ongoing restoration effort. To identify candidate genes conferring blight resistance, we have performed resequencing of bacterial artificial chromosomes (BACs) spanning three blight resistance QTL regions. Comparison of the C. mollissima reference genome to ten other plant reference genomes has revealed major regions of conserved macro- and micro-synteny with other long-lived woody angiosperms, particularly peach, grape and poplar. To further the utilization and integration of genomic resources from chestnut and other hardwood tree species, a suite of online tools is now available, including a genome browser, a gene editor and a genome comparison tool at the Hardwood Genomics website (http://hardwoodgenomics.org). New initiatives utilizing these genomic resources are underway, including genotyping-by-sequencing (GBS) of thousands of trees in the American Chestnut Foundation backcross breeding program (http://www.acf.org/) and implementation of genomic selection.