Fig. 3.

Synteny between japonica chromosome 5 (OsJ5) and related chromosomes in indica (OSI1 and OSI5). This figure shows the syntenic blocks between chromosome 5 of O. sativa japonica with chromosomes 1 and 5 of indica (innermost section of the figure). The bar plot shows SNP density in the genomic region based on SNPs common to five indica re-sequenced genomes. Blue lines represent SNP densities ≥5 per kb, while orange lines represent SNP densities <5 per kb. SNP density was calculated separately for every 100kb. Mapped grain quality QTLs are shown next to the SNP density bar plots. Mapped QTLs whose lengths are between 1Mb and 5Mb are represented as lines, while fine-mapped QTLs (size <1Mb) are represented as triangles. Genomic hotspots that have the highest SNP densities can be found on chromosomes 1 and 5 of indica as well as japonica. These hotspots coincide with several grain quality QTLs, including the recently cloned chalk gene H ⁺ -translocating pyrophosphatase.