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Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species maize (Zea mays L.). Previous studies have identified numerous quantitative trait loci (QTL) and genetic sequences associated with flowering time. However, beyond the nuclear genome, the maternal cytoplasm may also be involved in the regulation of flowering time. The objectives of this study were to locate the associated QTL based on a special mating design and to verify the hypothesis that the maternal cytoplasm may also contribute to the variation in flowering time. In the present study, a reciprocal mating design was conducted to generate F2 mapping populations comprising 120 F2 plants from the direct cross (JB × Y53) and 120 F2 plants from the reciprocal cross (Y53 × JB). F2:3 mapping populations were further generated with 91 direct F2:3 families and 120 reciprocal F2:3 families (10 plants per family). The days to tassel (DTT) and the days to pollen shed (DPS) of the above F2 and F2:3 mapping populations were evaluated in the same field and at the same experimental station in 2007 and 2008. A genetic linkage map with 154 microsatellite markers was constructed that covered 1735 cM of the maize genome with an average marker spacing of 11.3 cM. A joint analysis method incorporating the cytonuclear interaction mapping approach was proposed and performed to detect the QTL affecting DTT and DPS. As a result, eight and 11 QTL were detected for DTT and DPS, respectively. Interestingly, although the cytoplasmic effects were not significant between the direct and reciprocal populations, the interactions among the cytoplasm and the QTL were detected for both DTT and DPS. In the present study, four and eight cytonuclear epistatic QTL significantly contributed to the variation in DTT and DPS, respectively. Importantly, most of these cytonuclear epistatic QTL cannot be detected using the interval mapping method. These results suggest that the maternal cytoplasm might also be involved in the regulation of flowering time by interacting with nuclear genes in maize.

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