Digitaria genome analyses indicate introgression may drive local adaptation and herbicide resistance

Crabgrasses (Digitaria spp.) rank among the most invasive upland weeds globally, exhibiting remarkable ecological plasticity. To uncover the genomic basis underlying their weediness and environmental adaptability, we generate a telomere-to-telomere (T2T) reference genome of Digitaria sanguinalis, along with its diploid progenitor D. radicosa and tetraploid progenitor D. milanjiana. In addition, we re-sequence 579 accessions collected from fields of 24 grain-producing provinces in China. A phenotypic classification system for Digitaria species is developed by integrating genome-scale data with detailed morphological observations. Phylogenomic and comparative genomic analyses resolve the evolutionary history of Digitaria and reveal lineage-specific expansions in herbicide-associated gene families. Extensive sympatric introgression is observed within Digitaria, correlated with environmental selection. Through dose-response assay of 196 accessions, we identify 19 candidate genes associated with herbicide resistance, including DsSOH1. Haplotype analysis indicates that the resistant allele at DsSOH1 locus originated from D. ciliaris, suggesting a possible evolutionary contribution of introgression to the distribution of resistance-associated alleles. Together, our findings provide genomic insights into the evolutionary success of D. sanguinalis and offer resources for studying polyploid evolution and environmental adaptation as well as precision weed management in agroecosystems.