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Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. ‘Koshihikari’, which is a leading variety in Japan. We used Oryza sativa L. ‘Hong Xie Nuo’ as the donor parent and backcrossed with ‘Koshihikari’ four times, resulting in a near isogenic line (NIL) for black grains. A whole genome survey of the introgression line using DNA markers suggested that three regions, on chromosomes 1, 3 and 4 are associated with black pigmentation. The locus on chromosome 3 has not been identified previously. A mapping analysis with 546 F2 plants derived from a cross between the black rice NIL and ‘Koshihikari’ was evaluated. The results indicated that all three loci are essential for black pigmentation. We named these loci Kala1, Kala3 and Kala4. The black rice NIL was evaluated for eating quality and general agronomic traits. The eating quality was greatly superior to that of ‘Okunomurasaki’, an existing black rice variety. The isogenicity of the black rice NIL to ‘Koshihikari’ was very high.

Characterization of resistance genes is essential for the development of a new variety resistant to blast (Magnaporthe grisea) in rice (Oryza sativa L.). In this study, we found that an indica variety, Kasalath, harbored a resistance gene that showed a broad spectrum of resistance reactions against standard differential blast isolates from the Philippines and Japan. Quantitative trait locus (QTL) analysis was conducted using backcross inbred lines derived from crosses between Kasalath and the japonica cultivar, Koshihikari, to detect the QTL for blast resistance. QTLs were detected on chromosomes 6 and 8. Further, QTL analysis of chromosome segment substitution lines of Kasalath in the Koshihikari genetic background revealed that the Kasalath allele at the QTL on chromosome 6 strongly contributed to blast resistance. These results suggested that the gene locus might be identical to Pi13(t) that had already been reported. By marker-assisted breeding, a near-isogenic line, Koshihikari Toyama BL7, with a Kasalath chromosome segment containing Pi13(t) introduced into Koshihikari genetic background, was developed. The reaction of Koshihikari Toyama BL7 to the differential blast isolates indicated that Pi13(t) was a broad-spectrum and moderate resistance gene. Since Pi13(t) showed single-gene segregation and was characterized, the gene was re-designated as Pi13.

To advance the identification of quantitative trait loci (QTLs) to reduce Cd content in rice (Oryza sativa L.) grains and breed low-Cd cultivars, we developed a novel population consisting of 46 chromosome segment substitution lines (CSSLs) in which donor segments of LAC23, a cultivar reported to have a low grain Cd content, were substituted into the Koshihikari genetic background. The parental cultivars and 32 CSSLs (the minimum set required for whole-genome coverage) were grown in two fields with different natural levels of soil Cd. QTL mapping by single-marker analysis using ANOVA indicated that eight chromosomal regions were associated with grain Cd content and detected a major QTL (qlGCd3) with a high F-test value in both fields (F = 9.19 and 5.60) on the long arm of chromosome 3. The LAC23 allele at qlGCd3 was associated with reduced grain Cd levels and appeared to reduce Cd transport from the shoots to the grains. Fine substitution mapping delimited qlGCd3 to a 3.5-Mbp region. Our results suggest that the low-Cd trait of LAC23 is controlled by multiple QTLs, and qlGCd3 is a promising candidate QTL to reduce the Cd level of rice grain.