Sexual compatibility requires self vs. non-self recognition. Genetically, two compatibility or mating-type systems govern recognition In heterothallic basidiomycete fungi such as the edible and woodrotting mushrooms and the economically important rust and smut phytopathogens. A bipolar system is defined by a single genetic locus (MAT) that can have two or multiple alleles. A tetrapolar system has two loci, each with two or more specificities. We have employed two species from the genus Usuilago (smut fungi) to discover a molecular explanation for the genetic difference in mating systems. Ustilago maydis, a tetrapolar species, has two genetically unlinked loci that encode the distinct mating functions of cell fusion (a locus) and subsequent sexual development and pathogenicity (b locus). We have recently described a b locus in a bipolar species, Ustiago hordei, wherein the existence of an a locus has been suspected, but not demonstrated. We report here the doning of an allele of the a locus (al) from U. hordei and the discovery that physical linkage ofthe a and b loci in this bipolar fungus accounts for the distinct mating system. Linkage establishes a large complex MAT locus in U. hordei; this locus appears to be in a region suppressed for recombination.A hallmark of the heterothallic basidiomycete fungi is the fusion of cells of different compatibility to form a dikaryotic mycelium in which each cell contains a pair of nuclei. The interaction of two non-self nuclei within one cell triggers a program of sexual development (1-5). Among the homobasidiomycetes, which include the mushrooms such as Schizophyllum commune and Coprinus cinereus (6, 7), w65% ofthe species regulate sexual compatibility genetically via a tetrapolar (bifactorial) mating system. In these fungi, two genetic loci, each with two or more allelic specificities, control sexual development. Approximately 25% of the species have a bipolar (unifactorial) mating system in which compatibility is governed by a single genetic locus. In the bipolar species, this locus can have two or multiple alleles, the latter being common in the homobasidiomycetes and the non-parasitic heterobasidiomycetes. The remaining 10% consist of homothallic species (6,8). Among the parasitic heterobasidiomycetes, such as the phytopathogenic rust, bunt, and smut fungi, the diallelic bipolar mating system is predominant with certain exceptions (9, 10). These exceptions include a multiallelic bipolar system for the bunt fungus Tilletia controversa (11) and the occurrence of a tetrapolar mating system in several smut species including Ustilago maydis and Ustilago longissima (10, 12). To our knowledge, the molecular mechanisms underlying the genetic differences between these mating systems have heretofore been unknown.Mating and dikaryon formation are intricately connected with pathogenicity in the smut fungi, and the mating-type loci in the tetrapolar smut pathogen U. maydis have recently been isolated and characterized (10,(13)(14)(15)(16)(17)(18)(19). The a locus has two s...