The genome of Lolium multiflorum reveals the genetic architecture of paraquat resistance

- Herbicide resistance in agricultural weeds has become one of the greatest challenges for sustainable crop production. The repeated evolution of herbicide resistance provides an excellent opportunity to study the genetic and physiological basis of the resistance phenotype and the evolutionary responses to human-mediated selection pressures. Lolium multiflorum is a ubiquitous weed that has evolved herbicide resistance repeatedly around the world in various cropping systems. - We assembled and annotated a chromosome-scale genome for L. multiflorum and elucidated the genetic architecture of paraquat resistance by performing quantitative trait loci analysis, genome-wide association studies, genetic divergence analysis, and transcriptome analyses from paraquat-resistant and -susceptible L. multiflorum populations. - Results suggested that two regions of chromosome 5 were associated with paraquat resistance. The regions contain candidate genes that encode cellular transport functions, including a novel multidrug and toxin extrusion (MATE) protein, and a cation transporter previously shown to interact with polyamines. - Our results reveal the genetic architecture of paraquat resistance and identified promising candidate genes for future functional studies. Given that L. multiflorum is a weed and a cultivated crop species, the genomic resources generated will prove valuable to a wide spectrum of the plant science community.