Using ethyl methanesulfonate (EMS) mutagenesis, we isolated an erect panicle mutant, R1338, from indica heavy-panicle restorer Shuhui498. Compared with wild type control, the mutant displayed dwarfism, erect and short panicle, short primary panicle branch, increased grain density, short grain length and increased grain thickness. In addition, the erect panicle architecture of R1388 resulted in significant decreased bending moment and increased resistance to panicle bending. Histocytological analysis indicated that the diameter of uppermost internode, cellulose content and lignin content play important roles in resistance to panicle bending. Genetic analysis revealed that the mutant phenotype was controlled by a semi-dominant nuclear gene. With resequencing and MutMap analysis strategy, we found that one SNP from A to G at the seventh exon of DEP2 resulted in the 928(th) amino acid substitution from arginine (AGG) to glycine (GGG) in R1338 mutant. Considering the phenotype of other dep2 mutants, the phenotype of R1338 was likely to be caused by the SNP in DEP2. The mutant R1338 and wild type were crossed with several sterile lines which respectively had different panicle types, the combinations generated from R1338 and curve panicle sterile lines showed semi-erect panicle, higher seed setting percentage and heterosis, and the combinations generated from R1388 and erect panicle sterile line with DEP1 showed erect panicle by gene additive effect. Moreover, the combinations with semi-erect panicle had superior light transmittance and stronger light intensity, which improved efficiency of light utilization to intermediate and subjacent leaves compared to the combinations with curved panicle. This study provides a good strategy to solve the problem of population density in three-line hybrid rice.