Abstract
Whole genome sequencing of Japonica cultivar, Koshihikari, by using next-generation sequencing technology, was performed to discover comprehensive set of SNPs and enhance potential power of allele mining among Japonica cultivars. One elite cultivar, Koshihikari was analyzed with Solexa Genome Analyzer, with the depth of x23 (8.9 GB) and unique read sequences were mapped on the reference genome of Nipponbare with x15 depth (5.8 GB). Resultant consensus sequence of Koshihikari covered 79.9% of the reference Nipponbare sequences. 67,051 SNPs were detected from the comparison of these two sequences. However, distribution of SNPs is not equally among the chromosomes. This unequal distribution might be caused by genetic bottleneck of Japonica or possibly due to the lineage of particular cultivars used. These candidate SNPs detected were also validated by using array-based SNP detection system. The SNP genotyping array was used to determine pedigree haplotype of Japanese cultivars and landraces.
