Natural variation in the OsAFB2 promoter enhances rice seedling emergence under submergence

Seedling emergence is a key adaptive trait for water direct-seeded rice, yet its genetic basis remains poorly understood and elite alleles are limited. Here, a genome-wide association study of 307 rice accessions identifies qSLS4, a locus controlling shoot elongation during seedling emergence under submergence. OsAFB2 encodes an auxin receptor and is the causal gene for qSLS4. Its knockout promotes shoot elongation by increasing cell length and cell number, thereby improving seedling emergence rather than promoting coleoptile elongation, and also reduces plant height with only a minor effect on yield per plant. Expression and pharmacological analyses suggest that OsAFB2 affects the final emergence phenotype through auxin-related regulation. In a candidate gene association analysis, a single nucleotide substitution (C to A) at -941 bp in the promoter of OsAFB2 is found to alter its expression level and contribute to variation in seedling emergence. OsDREB6 preferentially activates the OsAFB2^HapC promoter, whereas this substitution weakens the activation, resulting in lower expression and enhanced seedling emergence in OsAFB2^HapA. Together, these findings establish that OsAFB2 acts as a negative regulator of rice seedling emergence and uncover a promoter variant with potential value for improving water direct-seeded rice.