The Digitaria genomes reveal local adaption and herbicide resistance mediated by introgression

Crabgrasses ( Digitaria spp.), the most problematic upland weeds, are well-documented for their broad-spectrum herbicide resistance and ecological adaptability. The genetic mechanism of these adaptive traits remains largely unexplored. We assembled three telomere-to-telomere (T2T) reference genomes of the globally invasive species Digitaria sanguinalis , along with its diploid and tetraploid progenitors. In addition, we re-sequenced 579 accessions from sympatric populations sampled over the past decade, coupled with nicosulfuron (an ALS inhibitor herbicide) resistance phenotyping. Genomic analysis of D. sanguinalis revealed adaptation driven by polyploidization. Extensive sampling across Digitaria species uncovered widespread introgression among sympatric lineages. Notably, introgression contributed to enhanced cold tolerance, likely facilitating adaptation to northern environments. Dose-response assays revealed a recent surge in nicosulfuron resistance in D. sanguinalis , which cannot be explained by target-site mutations alone. Genome-wide association study identified 40 SNPs significantly associated with non-target-site resistance (NTSR). We further identified a recently introgressed region from sympatric D. ciliaris associated with NTSR. Moreover, herbicide-resistant populations exhibited a higher number of introgressed genomic blocks compared to susceptible ones. These findings reveal adaptive introgression from relatives as a key source of variation, promoting rapid adaptation under selection pressure.