Interspecific and intersubspecific crosses have been an important strategy for rice breeding programs to obtain useful characters by expanding genetic diversity. However, the wide cross routinely causes undesirable characters in rice, such as spikelet sterility and poor quality. In this study, we developed near-isogenic lines of R-gene (Xa4+xa5+Xa21+Pi40+Bph18) introgression population to investigate the genetic relationship between the occurrence of poor characters and R-genes induced by MAS. The ANOVA analysis revealed that Pi40, Bph18, and Xa4 were associated with spikelet fertility (SF), ratio of ripened grain (RRG), third internode length (TIL), panicle extraction (PE), and protein content (Pro), whereas others showed no association with the 14 traits tested. In the three-way ANOVA, the impact of two R-genes (Pi40 and Bph18) on the poor characters was independent, with no interaction with others. Quantitative trait locus (QTL) analysis identified QTLs for PE and TIL traits near Pi40, and in particular, QTLs for five traits (SF, RRG, TIL, PE, and Pro) were negatively affected around Bph18. The occurrence of a poor character in R-gene pyramiding lines could be associated with linkage drag caused by the Bph18 gene. We speculate that the development of DNA markers that effectively eliminate poor characters will not only improve breeding efficiency using MAS, but will also help improve traits of japonica rice through wide crossing.