Genetic dissection and transcriptomic analysis of a novel high‐tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil‐type Rice (Milyang23)

population. We identified and fine-mapped two major loci, qHT1 and qHT6, where alleles from Hapcheonaengmi3 induce the HT phenotype in the Milyang23 background. Advanced fine mapping facilitated by window-size adjustments further resolved qHT1 into two candidate intervals (qHT1.1 and qHT1.2). Candidate gene analysis highlighted a putative SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor within qHT6. Furthermore, transcriptomic profiling of HT plants uncovered extensive reprogramming of hormone signaling, specifically affecting the gibberellin, auxin, and cytokinin pathways. Notably, the miR156-SPL module, previously implicated in bushy tillering, exhibited significant expression changes, identifying it as a key regulatory candidate. These findings provide crucial insights into a novel polygenic mechanism controlling rice tillering and highlight the value of cryptic variation in weedy rice.