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

Rice (Oryza sativa L.) tillering is a critical determinant of grain yield, yet the genetic mechanisms underlying non-productive tillers remain poorly understood. Here, we report a novel high-tillering (HT) phenotype derived from a cross between the elite cultivar Milyang23 and weedy rice Hapcheonaengmi3. The HT phenotype was absent in parental lines, suggesting it arises from unique allelic interactions. To elucidate the genetic basis of HT, we conducted quantitative trait locus sequencing and linkage analysis using recombinant inbred lines and an F2 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.