Researches on genetic basis of spikelets per panicle (SPP) and grain weight (TGW) have received much focus because of their contribution to rice yield. This study was conducted to fine-map QTL for spikelets per panicle (SPP) and 1,000-grain weight (TGW) using a near isogenic line (NIL), IL28 developed by introgressing chromosomal segments of the cultivar ‘Moroberekan’ into the cultivar ‘Ilpum’. Il28 showed a significant increase in the number of spikelets per panicle (SPP) and 1,000-grain weight (TGW) compared to the recurrent parent, Ilpum. QTL analysis in the F2 population derived from a cross between IL28 and Ilpum indicated that both qSPP6 and qTGW6 are located in the interval RM3430–RM20580. Substitution mapping with 50 F3:4:5 lines showed that qSPP6 was localized within 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 shows 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 compared to Ilpum.
Because the Moroberekan alleles for SPP and TGW have been shown to be beneficial in the genetic background of Ilpum, 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.