Optimizing the balance of panicle-related traits, such as the number of primary branches, secondary branches and panicle length, is needed for improving the number of spikelets per panicle in rice. These traits are affected by several genes which are expressed during panicle development stage. In this study, we investigated genetic information about several genes that were previously reported to control panicle development. Then, candidate gene association analysis was conducted to identify polymorphic sites associated with panicle-related traits. The results of association analysis showed that 35 polymorphic sites within 6 genes were significantly associated with panicle-related traits. Combinations of favorable or non-favorable allele were divided into 4 cluster. Of these, the cluster C which consisted of indica and tong-il type varieties had the largest number of favorable alleles. This cluster showed on average higher the number of spikelets per panicle than the other 3 clusters, implying that allele combination of this cluster could lead to increase in the number of spikelets per panicle. Therefore, the favorable alleles and combination identified in this study can be used as a functional marker set for molecular breeding program to improve the number of spikelets per panicle.
