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Generally, there is only one seed in each floret of the common wheat (Triticum aestivum L.). However, DUOII is a multi-ovary variety that has 2–3 pistils and 3 stamens. The genetics of DUOII are very stable; and it can set 2–3 seeds similar to mono-ovary wheat. Previously, we found that special heterogeneous cytoplasm influenced the expression of the multi-ovary gene. To study the genetics governing DUOII under the influence of special heterogeneous cytoplasm, we made a reciprocal cross between DUOII and TeZhiI, which has the nucleus of common wheat with the cytoplasm of Aegilops. By investigating the multi-ovary trait in the reciprocal cross and the F2, F3, BC1, and BC1F1 offspring, we found that the DUOII multi-ovary trait was controlled by a dominant gene, and that the special heterogeneous cytoplasm of TeZhiI suppressed the expression of this gene. In addition, the special heterogeneous cytoplasm could only suppress the expression of the heterozygous, but not homozygous, dominant multi-ovary gene, which resulted in the heterozygous dominant multi-ovary plant producing a mono-ovary phenotype, and the homozygous dominant plant producing the multi-ovary trait. The multi-ovary trait of DUOII was determined by nuclear-cytoplasm interactions and that the special heterogeneous cytoplasm of TZI could suppress the expression of the multi-ovary gene in a new particular way. Hence, the DUOII is an ideal model for further research into nuclear-cytoplasm interactions, and the genetic basis of DUOII provides a theoretical foundation for the practical application of the multi-ovary trait in hybrid wheat. [ABSTRACT FROM AUTHOR]