Abstract: The Gametophyte factor1 (Ga1) locus in maize confers unilateral cross‐incompatibility (UCI), and it is controlled by both pollen and silk‐specific determinants. Although the Ga1 locus has been reported for more than a century and is widely utilized in maize breeding programs, only the pollen‐specific ZmGa1P has been shown to function as a male determinant; thus, the genomic structure of the Ga1 locus and all the determinants that control UCI at this locus have not yet been fully characterized. Here, we used map‐based cloning to confirm the determinants of UCI at the Ga1 locus and maize pan‐genome sequence data to characterize the genomic structure of the Ga1 locus. The Ga1 locus comprises one silk‐expressed pectin methylesterase gene (PME, ZmGa1F) and eight pollen‐ expressed PMEs (ZmGa1P and ZmGa1PL1‐7). Knockout of ZmGa1F in Ga1/Ga1 lines leads to the complete loss of the female barrier function. The expression of individual ZmGa1PL genes in a ga1/ga1 background endows ga1 pollen with the ability to overcome the female barrier of the Ga1 locus. These findings, combined with genomic data and genetic analyses, indicate that the Ga1 locus is modulated by a single female determinant and multiple male determinants, which are tightly linked. The results of this study provide valuable insights into the genomic structure of the Ga2 and Tcb1 loci and will aid applications of these loci in maize breeding programs.

Key words: Gametophyte factor1, maize, unilateral cross‐ incompatibility, ZmGa1F, ZmGa1PL