Genetic dissection of black grain rice by the development of a near isogenic line.

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.

Detection of QTLs to reduce cadmium content in rice grains using LAC23/Koshihikari chromosome segment substitution lines.

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.