Location: Plant Physiology and Genetics ResearchTitle: Genomic diversity and phylogenetic relationships in the genus Parthenium (Asteraceae)
|ILUT, DANIEL - Cornell University - New York|
|COSTICH, DENISE - International Maize & Wheat Improvement Center (CIMMYT)|
|FRIEBE, BERND - Kansas State University|
|JENKS, MATTHEW - West Virginia University|
|GORE, MICHAEL - Cornell University - New York|
Submitted to: Industrial Crops and Products
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2015
Publication Date: 8/24/2015
Citation: Ilut, D.C., Sanchez, P.L., Costich, D.E., Friebe, B., Coffelt, T.A., Dyer, J.M., Jenks, M.A., Gore, M.A. 2015. Genomic diversity and phylogenetic relationships in the genus Parthenium (Asteraceae). Industrial Crops and Products. 76:920-929.
Interpretive Summary: Guayule is a perennial hardwood shrub native to the southwestern United States and Mexico that holds great promise as a sustainable source of natural rubber and hypoallergenic latex. The amount of rubber in the plant, however, is quite low, and thus research is required to increase plant productivity. Plant breeding offers one approach to increase rubber yields, but any successful breeding program requires diverse, well-defined individuals that can be used for plant crossing and introduction of new and/or improved traits. In an effort to characterize the diversity of guayule plants available for breeding, scientists at Cornell University, the ARS lab in Maricopa, Arizona, the International Maize and Wheat Improvement Center (CIMMYT), Kansas State University, and West Virginia University determined a portion of the DNA sequences for many individual guayule plants and closely related plant species. An analysis of the DNA sequences revealed the evolutionary relationships between the individuals and also identified many subtle differences in DNA sequence that could be used as “markers” in plant breeding experiments. The results of these studies provide the most detailed description yet for guayule diversity and will be instrumental in future efforts to increase rubber content of guayule through plant breeding.
Technical Abstract: Guayule (Parthenium argentatum A. Gray) is a perennial hardwood shrub native to the North American Chihuahuan Desert that holds promise as a sustainable source of natural rubber and hypoallergenic latex. The improvement of guayule for commercial-scale production could be potentially accelerated through genomics-assisted breeding, but such a strategy is severely limited by a paucity of genetic and genomic tools and resources. To that end, we used genotyping-by-sequencing (GBS) to simultaneously identify and genotype tens of thousands of single-nucleotide polymorphism (SNP) markers across 62 plant samples from seven wild and cultivated guayule, three Parthenium interspecific hybrids, four mariola (Parthenium incanum Kunth), and one wild quinine (Parthenium integrifolium L.) accession(s) that have been characterized for ploidy level and nuclear genome size in this and a prior study. Phylogenetic analysis using the SNP data identified at least two distinct sources of guayule breeding material in the cultivated accessions, previously unknown multi-species hybrids within two Parthenium hybrid cultivars, and guayule/mariola hybrids within one guayule and one mariola wild collected accession. Similar to previously reported results for guayule and mariola, we observed aneuploidy and multiple ploidy levels among individual plants (mixed ploidy) within three Parthenium interspecific hybrid accessions newly characterized in this study. Genome size characterization of wild quinine, a first for this species, found an estimated haploid nuclear genome size (5757 Mb) for the tetraploid (2n=4x=72) accession that was more than 1.5-fold larger than that of tetraploid (2n=4x=72) guayule or mariola. Together, these results further underscore the need for a comprehensive characterization of available guayule germplasm and sister taxa with both SNP markers and flow cytometry, illustrate the novel utility of GBS for the genus Parthenium, and lay the foundation for genomics-assisted breeding in guayule.