Development of Genomic Resources for Guayule (Parthenium argentatum A. Gray)

Guayule is a perennial hardwood shrub native to the North American Chihuahuan desert that produces significant quantities of natural rubber, and it has been intermittently cultivated and studied as a source of domestic rubber and hypoallergenic latex throughout the 20th century.  However, in order to increase its yield potential and suitability for commercialization, genetic improvement through modern plant breeding is necessary.  Natural variation for ploidy level is extensive among individuals in wild guayule populations as well as breeding germplasm, the species reproduces by facultative apomixis (diplospory type), and has a highly variable number of chromosomes.  Therefore, extensive genetic and genomic characterization is needed for a successful crop improvement program.  To that end, our project has undertaken the de novo genome sequencing of the diploid (2n=2x=36) guayule accession, PI 478663, to nearly 10X coverage.  In addition, we are conducting genotyping-by-sequencing of the near complete guayule germplasm collection available from the U.S. National Plant Germplasm System, followed by low-coverage whole-genome resequencing of several founders that contributed significantly to public guayule breeding programs. The SNPs identified in this research will be used to study genetic structure and diversity among guayule accessions and construct a custom genotyping array for the guayule community. We present here the resources developed so far, as well as the novel bioinformatic approaches created to address the unique challenges of this high heterozygousity and variable ploidy species.