Ginger genome enables identification of SMPED1 causing sex-phase synchrony and outcrossing in a flowering plant

In many flowering plants, male and female reproductive organs mature at different times to avoid self-pollination, a phenomenon termed dichogamy. Most dichogamous species are either protandrous (male function first) or protogynous (female function first), making this strategy difficult to be studied. However, in the ginger Alpinia mutica , protandrous and protogynous morphotypes co-occur within populations and cross-pollinate one another. Here, we demonstrate that a single Mendelian locus with a dominant allele governing protogyny controls sexual polymorphism. We used haplotype-resolved genomes and population genomics to identify the dichogamy-determining region, revealing a large deletion in the protandrous morphotype. STYLE MOVEMENT AND POLLEN EARLY DISPERSAL 1 ( SMPED1 ), located adjacent to the deletion,governs the timing of anther dehiscence and style movement. SMPED1 is widespread among angiosperms and likely has a conserved function. Our findings represent the first genetic characterization of a key mating system gene controlling the synchrony of sex organs in flowering plants.