Genomic insights into herbicide resistance evolution in allopolyploid Monochoria korsakowii

SUMMARY Monochoria korsakowii , a common broadleaf weed in rice paddies, has evolved resistance to acetolactate synthase‐inhibiting herbicides (e.g., bensulfuron‐methyl BSM). However, genomic information for M. korsakowii remains scarce. Here, the first chromosome‐scale genome assembly of the allotetraploid M. korsakowii is presented. Comparative genomics reveals a complex genomic architecture that explains its enhanced adaptation to herbicides. No evidence of global subgenome dominance is found; instead, the two subgenomes exhibit functional specialization. Genes preferentially expressed in subgenome A are enriched in pathways related to maintaining energy and physiological homeostasis, whereas those in subgenome B are mainly associated with non‐target‐site pathways, particularly reactive oxygen species scavenging. Furthermore, sequence analysis shows that tandem duplicates are significantly enriched for herbicide metabolism‐related functions, suggesting a potential role for tandem duplication in the evolution of herbicide resistance. Transcriptomic and functional analyses identify a glutathione S‐transferase gene ( MkoA03G003170 ) as a key factor conferring metabolic resistance to BSM. This study identifies polyploidy‐induced genomic plasticity as a potential factor in resistance, providing a foundational genomic resource for understanding weed adaptation and developing sustainable management strategies.