Panicle architecture is closely related to yield formation. The qPE9-1 gene has been proved to be widely used in high-yield rice cultivar developments, conferring erect panicle character in japonica rice. Recently, qPE9-1 has been successfully cloned; however, the genetic effect on grain yield per plant of the erect panicle allele qPE9-1 is controversial yet. In the present study, a drooping panicle parent Nongken 57, carrying qpe9-1 allele, was used as recurrent parent to successively backcross to a typical erect panicle line from the double haploid (DH) population (Wuyunjing 8/Nongken 57), which was previously shown to carry qPE9-1 allele. Thus a pair of near-isogenic lines (NILs) was developed. The comparison of agronomic traits between the NILs showed that, when qpe9-1 was replaced by qPE9-1, the panicle architecture was changed from drooping to erect; moreover, the panicle length, plant height, 1000-grain weight and the tillers were significantly decreased, consequently resulting in the dramatic decrease of grain yield per plant by 30%. Therefore, we concluded that the qPE9-1 was a major factor controlling panicle architecture, and qPE9-1 had pleiotropic nature, with negative effects on grain yield per plant. This result strongly suggests that the erect panicle allele qPE9-1 should be used together with other favorable genes in the high-yield breeding practice. In addition, the effect of qPE9-1 on eating and cooking quality was also discussed in the present study.