A BLH12-KN1 transcriptional module regulates embryo size in maize.

UNLABELLED: Embryo development is a critical determinant of plant growth and a major contributor to grain nutritional value in maize. In this study, we identified natural variations in BLH12, which encodes a BEL1-like homeodomain transcription factor, that is significantly associated with embryo size in maize. SNP-506, located in the 5' untranslated region, and SNP3670 (A-to-G), resulting in a glutamine-to-arginine substitution in the last exon, were shown to be the causal variants of BLH12 for embryo size. Loss-of-function of BLH12 reduced embryo length, width, and thickness, leading to decreased embryo size and weight. Histological analysis revealed that BLH12 acts from the late embryo proper stage onward and sustains its regulatory activity throughout subsequent development. The knockout of KN1, an interacting partner of BLH12, exhibited comparable defects in embryo morphology and kernel traits. Transcriptomic profiling along with published KN1 ChIP-seq targets further revealed a potential cooperative regulatory relationship between BLH12 and KN1 during maize embryo development. These findings uncover BLH12 as a key regulator of maize embryogenesis and provide a promising target for improving kernel nutrients in maize breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01716-y.