Characterization of a genomic region that maintains chlorophyll and nitrogen contents during ripening in a high-yielding stay-green rice cultivar

The high-yielding indica × japonica rice (Oryza sativa L.) cultivar Akenohoshi tends to maintain a higher photosynthetic rate during ripening owing to its higher nitrogen accumulation and nitrogen partitioning to leaves than the commercial japonica cultivar Koshihikari. By using recombinant inbred lines derived from a cross between Akenohoshi and Koshihikari, we detected at least 6 quantitative trait loci (QTLs) for maintaining higher leaf chlorophyll content, 4 QTLs for nitrogen content, and 5 QTLs for the rate of nitrogen transport to shoots during ripening in the paddy field. Then we developed two chromosome segment substitution lines carrying Akenohoshi segments on the short arm of chromosome 3, where the QTLs for chlorophyll content reduction were clustered, in the Koshihikari genetic background. The lines showed higher rate of nitrogen transport to shoots, leaf chlorophyll and nitrogen contents, and therefore a higher rate of leaf photosynthesis, than Koshihikari. We concluded that a 7.7-Mb region present in both two lines, named qCHR1, is important for maintaining chlorophyll and nitrogen contents during senescence. The Akenohoshi allele at qCHR1 increased nitrogen accumulation and nitrogen partitioning to leaves during ripening, but did not change yield.