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Background  High grain yield is one of the most important traits requiring improvement in rice breeding programs. Consequently, the genetic basis of spikelets per panicle (SPP) and grain weight (TGW) have received much research focus because of their importance in rice yield.    Results  In this study, IL28, which is a near isogenic line (NIL) developed by introgressing chromosomal segments of the cultivar ‘Moroberekan’ into the cultivar ‘Ilpumbyeo’, showed a significant increase in the number of spikelets per panicle (SPP) and 1,000-grain weight (TGW) compared to the recurrent parent, Ilpumbyeo. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that both  qSPP6  and  qTGW6  are located in the interval RM3430–RM20580. Following substitution mapping with 50 F 3:4:5  lines,  qSPP6  was mapped to a 429-kb interval between RM20521 and InDel-1, while  qTGW6  was mapped to a 37.85-kb interval between InDel-1 and SNP--3 based on the  japonica  genome sequence. This result indicates that  qSPP6  and  qTGW6  are different genes. Yield trials with substitution lines indicated that lines harboring the homozygous Moroberekan segment at both the  qSPP6  and  qTGW6  region showed significantly higher grain yield than Ilpumbyeo.    Conclusion  Because the Moroberekan alleles for SPP and TGW have been shown to be beneficial in the genetic background of Ilpumbyeo, both the  qSPP6  and  qTGW6  alleles might prove valuable in improving rice yields. Closely linked SSR markers are expected to facilitate the cloning of genes that underlie these QTLs, as well as with marker-assisted selection for variation in SPP and TGW in rice breeding programs.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-014-0014-5) contains supplementary material, which is available to authorized users.

High-density mapping of quantitative trait loci for grain-weight and spikelet number in rice