Persistence of ALS S653N Resistance Alleles on a Cultivar-Type Haplotype in Weedy Rice

Weedy rice (Oryza sativa L.) is a troublesome invasive weed in rice fields. Control is challenging because weedy and cultivated rice are genetically similar. Moreover, Clearfield technology contributes to imidazolinone (IMI)-resistant weedy rice biotypes. This study aimed to determine the frequency of the acetolactate synthase (ALS) S653N resistance allele in weedy rice from northern Türkiye and the ALS haplotype on which it occurs. A total of 280 biotypes were collected between 2022 and 2023. Of these, 92 survived a 2× imazamox rate and were evaluated in dose–response assays. The ALS region conferring IMI resistance was sequenced in these survivors. The Clearfield substitution S653N was found in 64 of them. Linked silent SNPs placed S653N on the cultivar-type ALS haplotype: 63 of the 64 carriers shared the haplotype of the regional Clearfield cultivar. The crop-derived allele therefore persists in weedy rice, with no evidence of a region-level change in frequency since 2020–2021; the haplotype identifies the origin of the allele but cannot date the transfer. Mitigation in Clearfield systems requires integrated strategies, including dual imazamox applications, crop rotation, targeted spot spraying, stale seedbed preparation, and herbicide-resistant rice varieties such as Provisia or Roxy, none of which was tested here.