Genetic Dissection of Rice Allelopathy to Barnyardgrass Using a Sathi/Nongan RIL Population and QTL-Seq Analysis

Rice allelopathy offers potential for sustainable weed management, but its genetic basis remains poorly understood. We evaluated allelopathic activity in 172 F10 recombinant inbred lines (RILs) derived from strongly allelopathic Sathi and weakly allelopathic Nongan using barnyardgrass (Echinochloa crus-galli) as the receiver plant. Five barnyardgrass growth traits under co-cultivation with rice showed continuous variation, and shoot length was selected for QTL-seq. SNP-index analysis identified a candidate QTL, qALO8, at 22.1–24.8 Mb on chromosome 8. Among 103 annotated genes in this interval, Os08g0456200 (CYP92A6-like), Os08g0459600 (OPR7), and Os08g0465700 (CYP76M1) were initially prioritized based on their positions and annotations related to secondary metabolism. Sequence comparison between Sathi and Nongan identified no nonsynonymous substitutions in OPR7, one in CYP76M1, and four in CYP92A6-like. These findings identify qALO8 as a candidate QTL associated with rice allelopathic variation and prioritize CYP76M1 and CYP92A6-like for functional investigation.