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To find new QTLs responsible for kernel cracking resistance, we screened 50 CSSLs derived from the moderately resistant cultivar ‘Itadaki’ (O. sativa L.) and the donor O. rufipogon. Two lines, IRSL 30 and IRSL 37, were selected as resistant. QTL analyses of the percentage of cracked kernels (PCK) in F4 individuals derived from “Itadaki/IRSL 30” and “Itadaki/IRSL 37” identified a major QTL, qCR (Cracking Resistance) 8-2, at the same position on chromosome 8 in both populations. ‘IRSL 30’ and ‘IRSL 37’ had a reduced PCK. These results show that qCR8-2 is likely to be an important QTL for kernel cracking resistance. Both lines had long awns, linked to qCR8-2, but the awnless line ‘Chukei 19301’ was also derived from “Itadaki/IRSL 37”, so qCR8-2 is distinct from the gene for awn development. We consider that qCR8-2 will help in the breeding of new rice cultivars with high cracking resistance and in elucidating the physiological mechanism of kernel cracking.

It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars.

‘Tachisuzuka’ is a new rice (Oryza sativa L.) cultivar for whole-crop silage (WCS) use. Agronomic characters were recorded from 2007 to 2009. The culm length of Tachisuzuka was 11 cm longer than that of Kusanohoshi. The short panicle of Tachisuzuka was morphologically similar to that of the short panicle 1 (sp1) mutant. Tachisuzuka exhibited high lodging resistance in the yellow ripening stage, the optimal period for harvesting, and a month after yellow ripening. The straw yield of Tachisuzuka was remarkably higher than that of Kusanohoshi but its grain yield was lower. A portion of grains are undigested and excreted in feces by cattle fed with rice WCS, and this loss of nutrients should not be disregarded. The low grain/straw ratio of Tachisuzuka indicates that the loss of nutrients in cattle fed with Tachisuzuka WCS should be lower than with Kusanohoshi WCS. Low sugar content of rice plants is considered a cause of silage deterioration. The sugar content of Tachisuzuka was markedly higher than that of Kusanohoshi.

To identify the chromosomal regions controlling the eating quality of cooked rice, we performed a quantitative trait locus (QTL) analysis using 93 backcross inbred lines (BILs) and 39 chromosome segment substitution lines (CSSLs) derived from crosses between a japonica rice cultivar Koshihikari (glossier appearance, tasty, sticky and soft eating quality of rice when cooked) and an indica cultivar Kasalath (less glossy appearance, less sticky and hard eating quality of rice when cooked). We evaluated the eating quality of rice including overall evaluation (OE), glossiness (GL), taste (TA), stickiness (ST) and hardness (HA) in each line based on the sensory test of cooked rice. Twenty-one QTLs for eating quality were mapped to eight regions on chromosomes 1, 2, 3 (two regions), 6, 7, 9 and 10. The Koshihikari alleles at 19 out of 21 QTLs increased the eating quality, while the Kasalath alleles at the other two QTLs increased the eating quality. We also mapped the QTLs for chemical properties, such as amylose content (AC) and protein content (PC), which affected the eating quality. Four QTLs in the terminal region of the short arm of chromosome 3 and five QTLs on chromosome 6 for eating quality were mapped to the same region as that of the QTLs for AC. Three QTLs on chromosome 1 for eating quality were also mapped to the same region as that of a QTL for PC. The chromosome positions of the other QTLs for eating quality did not coincide with those of the QTLs for AC and PC. Six out of 21 QTLs for eating quality, qTA3, qOE6, qGL6, qTA6, qST6 and qHA6, were commonly identified by analysis using both BILs and CSSLs. One QTL, qTA3, was not a locus of AC, PC or known eating genes. Thus the QTL was mapped in the interval between the SSR markers RM1332 and RM6676 in the middle region of the short arm of chromosome 3 by fine mapping of three sub-CSSLs. Five QTLs, qOE6, qGL6, qTA6, qST6 and qHA6, seemed to be associated with the Waxy (Wx) gene located on chromosome 6.

The rice line WSS2 which was derived from the Vietnamese indica variety Tetep, displays a high partial resistance to sheath blight. Quantitative trait locus (QTL) analysis of the resistance using simple sequence repeat (SSR) and sequence-tagged site (STS) markers was conducted in a BC1F1 population derived from the cross Hinohikari/WSS2//Hinohikari. Sheath blight resistance in this population and its cross-parents was studied using syringe inoculation. Two QTLs for sheath blight resistance (qSB-3 and qSB-12) were identified on chromosomes 3 and 12. Their resistance alleles were derived from the resistant parent WSS2. These QTLs totally explained 29.6% of the phenotypic variation. Sheath blight resistance was significantly correlated with culm length and heading date. Among the QTLs for culm length and heading date, qCL-3 for culm length was located in the same region as qSB-3, and the remaining QTLs were not linked to qSB-12. Thus, it was reasonable to assume that qSB-12 would enable to breed a rice variety resistant to sheath blight.