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Plant height, heading date and number of spikelets per panicle are important agronomic traits of rice. They are complex quantitative traits. With the increasing use of molecular markers, high-density rice genetic linkage map has been successfully drawn. Meanwhile, statistical software has been enhanced. Therefore, QTL research has become easier. At the same time, QTL epistatic effects, which is an important factor affecting quantitative traits, has been deeply known by more and more people.In BC3F2 population derived from the cross Zhenshan97/Pokkali, a main effect QTL for plant height, designated Qphl, was located on chromosome 1, between MRG4382 and MRG0339. Its additive effect was 57.1 cm, dominant effect was 30.6 cm, could explain 90.3 percent of phenotypic variation. Ghd7 was also separated in this population. In this study, near isogenic line population which Ghd7 and Qphl were simultaneously segregated was constructed for their interaction analysis. The main results are as follows:1. In Qph1-population, QTL for plant height was still scanned between MRG4382 and MRG0339, the additive effect was 51.0 cm, the dominant effect was 26.6 cm, could explain 92.7 percent of phenotypic variation. Qphl was also found to affect the number of spikelets per panicle.2. In Qph1-Ghd7 population, plant height was significantly divided into high and low types. In the high phenotype and low phenotype, heading date both showed early, middle and late types. Segregation of plant height and heading date accorded with ratio of 3:1, spikelet per number presented a normal distribution.3. QTL analysis showed that, in Qphl-Ghd7 populations, Qph1 controlled both plant height and number of spikelets per panicle, while Ghd7 controlled heading date, plant height and number of spikelets per panicle.4. Epistatic interaction for plant height was revealed between Ghd7 and Qphl. Further analysis found additive×dominance and additive×additive effect affecting plant height. There was no epistatic interaction for spikelets per panicle between two QTLs.5. Pokkali carried positive alleles on Ghd7. Its effect for number of grains per panicle, plant height and heading date was equivalent to Zhenshan97 and Minghui63 allele. Ghd7 allele in Pokkali was beneficial to increase rice yield.
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