Fine mapping of qKDR3.06 identifies ZmBAK1a as a candidate gene controlling kernel dehydration rate in maize

Kernel moisture content (KMC) and kernel dehydration rate (KDR) strongly influence grain quality and suitability for mechanical harvesting in maize ( Zea mays ), yet the underlying genetic architecture is unclear. In this study, using a recombinant inbred line population phenotyped across four environments at 35, 42, 49, and 56 days after pollination (DAP), we identified 38 QTL associated with KMC and KDR, explaining 1.16–20.88% of the phenotypic variance. The major QTL qKDR3.06 accounted for 4.88–20.88% of the variance and was fine-mapped to a 219-kb interval in bin 3.06 of chromosome 3. Integrated parental sequence comparison, expression profiling, and regional association analysis identified ZmBAK1a (GRMZM5G815009), which encodes a brassinosteroid (BR) BAK1 family co-receptor, as the leading candidate gene in this interval. Five significant KDR-associated SNPs were located within this gene. A 202-bp InDel in the ZmBAK1a promoter distinguished the two parents, suggesting that this InDel is a causal regulatory variant. RT-qPCR revealed stage-specific differences in gene expression: the PH4CV allele (carrying the 202-bp deletion) showed lower ZmBAK1a expression at 28–40 DAP but significantly higher expression at 45 DAP than the KB020 allele. Consistent with this pattern, genotypes harboring the 202-bp deletion exhibited faster kernel dehydration in the AMP1 and AMP2 maize populations. Bioinformatic analysis identified a canonical salicylic acid (SA)-responsive cis -element within the deleted region. Given that BAK1 family genes regulate cell wall remodeling and water transport during grain maturation, we propose that ZmBAK1a influences late-stage kernel dehydration through BR-mediated signaling, with SA as a potential additional regulator. Our findings provide a functional marker and a novel gene target for breeding maize hybrids with rapidly dehydrating kernels.