Alleles Affecting 30 Traits for Productivity in Two Japonica Rice Varieties, Koshihikari and Nipponbare (Oryza sativa L.)

We identified chromosome regions affecting traits (CRATs) for 30 productivity-related traits using 2 sets of chromosome segment substitution lines (CSSLs). One was established using Nipponbare as the donor and Koshihikari as the background variety (Kos-Nip); and the other using Koshihikari as the donor and Nipponbare as the background (Nip-Kos). We identified 249 and 181 CRATs for 30 traits in Kos-Nip and Nip-Kos CSSLs, respectively. Donor alleles in 75 (Nipponbare) and 82 (Koshihikari) CRATs had positive effects on productivity. Among them, some CRATs represented superior effects as compared with the alleles in indica varieties Kasalath and Nona Bokra. On chromosome 1, a CRAT for panicle number (PN1) increased yield by about 1.4 times compared with Koshihikari. PN1 increased leaf area, while maintaining the SPAD value, which is an indicator of photosynthetic ability. Therefore, PN1 might have a pleiotropic effect on sink size and source ability, and thus could consequently improve yield. In only 29 CRATs for 13 traits (12% of total), corresponding CRATs with contrasting effects were detected in the 2 sets of CSSLs. These results suggested that the effect of a gene, might be affected by the genetic background. By using a database of single-nucleotide polymorphisms in Koshihikari and Nipponbare, we could narrow the candidate genes for 28/29 CRATs; to minimum 6 genes for CRAT related to plant height at the early stage and diameter at stem. Thus japonica rice could be a useful genetic donor for improving the productivity of another japonica variety.