Brunharo Caio A, Short Aidan W, Bobadilla Lucas K, Streisfeld Matthew A
Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA.
Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA.
Mol Ecol. 2025 May;34(10):e17775. doi: 10.1111/mec.17775. Epub 2025 Apr 26.
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 locus analysis, genome-wide association studies, genetic divergence analysis and transcriptome analyses from paraquat-resistant and -susceptible L. multiflorum plants. We identified two regions on chromosome 5 that were associated with paraquat resistance. These regions both showed evidence for positive selection among the resistant populations we sampled, but the effects of this selection on the genome differed, implying a complex evolutionary history. In addition, these regions contained candidate genes that encoded cellular transport functions, including a novel multidrug and toxin extrusion (MATE) protein and a cation transporter previously shown to interact with polyamines. 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. Our work contributes to a growing body of knowledge on the underlying evolutionary and ecological dynamics of rapid adaptation to strong anthropogenic selection pressure that could help initiate efforts to improve weed management practices in the long term for a more sustainable agriculture.
农业杂草中的除草剂抗性已成为可持续作物生产面临的最大挑战之一。除草剂抗性的反复进化为研究抗性表型的遗传和生理基础以及对人类介导的选择压力的进化反应提供了绝佳机会。多花黑麦草是一种常见杂草，在世界各地的各种种植系统中都反复进化出了除草剂抗性。我们组装并注释了多花黑麦草的染色体级基因组，并通过对多花黑麦草抗百草枯和感百草枯植株进行数量性状位点分析、全基因组关联研究、遗传分化分析和转录组分析，阐明了百草枯抗性的遗传结构。我们在5号染色体上鉴定出两个与百草枯抗性相关的区域。在我们采样的抗性群体中，这两个区域均显示出正选择的证据，但这种选择对基因组的影响不同，这意味着其进化历史复杂。此外，这些区域包含编码细胞转运功能的候选基因，包括一种新型多药和毒素外排（MATE）蛋白以及一种先前显示与多胺相互作用的阳离子转运蛋白。鉴于多花黑麦草既是一种杂草又是一种栽培作物品种，所产生的基因组资源将对广泛的植物科学界具有重要价值。我们的工作为关于快速适应强大人为选择压力的潜在进化和生态动态的知识体系增添了内容，这有助于长期启动改善杂草管理实践的努力，以实现更可持续的农业。
