Abstract: Successful establishment of direct-seeded rice (DSR) under deep sowing depends on rapid seedling emergence in darkness, mechanical impedance, and hypoxia conditions under which mesocotyl elongation becomes a decisive adaptive trait. Here, we integrate multi-year phenotyping, anatomy, phytohormone profiling, transcriptional analysis, and bulked segregant analysis sequencing (BSA-seq) in near-isogenic lines to dissect the regulatory basis of mesocotyl elongation and early seedling vigor under deep-sown DSR systems. Deep sowing selectively triggered mesocotyl elongation, enhanced aerenchyma formation, and elevated auxin and ethylene accumulation in tolerant genotypes, while susceptible lines failed to activate these responses. Light exposure strongly suppressed mesocotyl elongation, but this inhibition was attenuated under soil-imposed darkness and mechanical constraint. Genomic analyses converged on rice chromosome 7 as a central regulatory hub, with partially distinct loci governing mesocotyl elongation and integrated emergence. Successful emergence was associated with early repression of growth inhibitors (Myb30 and ICL) and depth-induced activation of a basic helix-loop-helix (bHLH) transcription factor (LOC_Os12g08025), linking transcriptional regulation with hormonal signaling and anatomical plasticity. Together, these findings define a narrow early developmental window in which coordinated hormonal, anatomical, and genomic programs enable mesocotyl-driven emergence under deep sowing, providing tractable targets for breeding rice cultivars adapted to mechanized DSR systems.

Key words: direct-seeded rice, deep sowing, mesocotyl elongation, seedling emergence, hormonal and anatomical regulation, bulked segregant analysis sequencing