Using Population Genomics to Combat Imperata cylindrica (L.) Beauv (Cogongrass, Speargrass), a Noxious Weed of Extensive Global Impact

Imperata cylindrica, a noxious weed in 73 countries, constitutes a significant threat to global sustainable agriculture. In the southeastern US alone, this species has invaded over 1.5 million acres. Repeated herbicide application fails to control Cogongrass. With global distribution, this species persists in a diversity of soil types, rainfall regimes, and temperature conditions. The objective of this work is to produce a population-genetic profile with sufficient resolution to correlate US Cogongrass genotypes to genotypes from the native range(s) in order to identify and genetically characterize potential host-specific biological controls.

Using the Illumina short-read sequencing platform, we have used a highly multiplexed genotyping by sequencing approach to survey over 500 field-collected Cogongrass samples from affected areas across the southeastern US.  Displaying significant synteny with Sorghum bicolor, we circumvented bioinformatic challenges for this non-model organism by using the sorghum genome as a proxy reference genome to facilitate single nucleotide polymorphism (SNP) identification. Phylogenetic and Bayesian population structure analysis with 2383 informative SNP markers suggest three major ecotypes of Cogongrass in the US. Our data indicate that each ecotype is highly clonal with minimal levels of admixture both within and among populations. Globally-distributed samples are now being acquired for sequence analysis in order to match genotypes observed in the US to genotypes from previously suggested regions of origin. A comprehensive sampling of globally-distributed genotypes has potential to benefit scientists in countries seeking sustainable approaches for Cogongrass control.