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To employ molecular marker-aided selection for developing japonica rice (Oryza sativa L.) cultivars with high yielding potential and good eating quality, we carried out QTL analysis for agronomic and grain traits using 231 recombinant inbred lines (RIL) from a cross between two temperate japonica cultivars, Suweon365 and Chucheongbyeo. A linkage map with 221 loci, including 134 simple sequence repeats (SSRs), 66 amplified fragment length polymorphisms (AFLPs), and 21 miniature inverted repeat transposable elements (MITEs)-anchored markers, was constructed covering 2,227 cM of the twelve rice chromosomes, with an average distance of 11.0 cM between markers. The proportion of polymorphic bands between parents averaged 19.5%, 12.9% and 42.3% for SSRs, AFLPs and MITEs, respectively. Construction of maps without AFLP or MITE markers indicated that expansion of this map is due to the incorporation of AFLP markers, and this result is consistent with previous reports. Twenty-seven QTLs for ten traits were identified over two years, and fourteen were consistently detected in two consecutive years. When the locations of each QTL detected in this study were compared with those in previous QTLs studies, eight QTLs for culm length, spikelets per panicle and, thickness, length and shape of grain, had not been reported in previous mapping studies, indicating potentially novel alleles of japonica rice. Interestingly, a cluster of seven QTLs, including heading date and grain morphology traits, was detected on the long arm of chromosome 7. The markers linked to these QTLs would be valuable in a marker-assisted breeding program for japonica cultivars.

QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.)