ARice is an important staple food in the world and rice yield is one of the main traits for rice breeding. Several genes involved in increasing the yield have been identified through map-based gene cloning within natural variations in rice. These identified genes are good targets for introducing a genetic trait in molecular breeding. Here, we chose five genes reported to be involved in increasing grain number per panicle in rice; Gn1a, dep1, Apo1, Ghd7, and Nal1. We developed In/Del markers for

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... Gn1a, and dep1, Apo1, and applied the reported SNP markers for Ghd7 and Nal1. We were easily able to examine the genotype of each gene on agarose gel. We tested the genotypes on 479 rice resources that we held with evaluated molecular markers. According to the genotype of each gene, rice resources were divided into 13 haplotypes, and most of the Indica and Japonica varieties were included in haplotypes 1 and 13, respectively. When we examined the effect of each gene on grain number per panicle and panicle number per plant, panicle number per plant in the yield negative allele group for each gene was reduced by approximately 0.3 to 0.8 compared to that in the yield positive allele group. However, the number of yield positive alleles for each gene was higher by about 21 to 27 grains per panicle than that of yield negative alleles. Although most of the varieties were grouped in haplotypes 1 and 13, we believe that this genotype information with evaluated molecular markers will be useful in rice breeding for increasing the yield with grain number per panicle.