Plant & Animal Genomes XVII Conference Plant & Animal Genomes XVII ConferenceJanuary 10-14, 2009
Town & Country Convention Center
San Diego, CA
Kaworu Ebana , Hideki Nagasaki , Maiko Nakajima , Toshio Yamamoto , Jun-ichi Yonemaru , Masahiro Yano
A large scale single nucleotide polymorphism (SNP) discovery has been conducted so far. Such efforts provided us a large set of SNPs among the rice accessions, enhancing our understanding of the association between nucleotide sequences and phenotypes. However, a small number of SNPs could be available among Japonica cultivars, in particular, temperate Japonica, although certain amount of naturally occurring variations have been observed. We have performed a whole genome sequencing of Japonica cultivar, Koshihikari, by using next-generation sequencing technology, 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 (illumina), with the depth of x 23 (8.9 GB) and unique read sequences were mapped on the reference genome of Nipponbare with x 15 depth (5.8 GB). Consensus sequence of Koshihikari covered 79.9% of the reference genome. 67,051 SNPs were detected from the comparison of these two sequences. The average number of SNPs/kb is 0.197 and this seems enough value for genetic analysis. These SNPs were validated by using Array-based SNP detection system and found to be only 10% of SNPs detected as false positive. Other cultivars will be sequenced to cover all the genetic variation of Japonica cultivar groups, because the distribution of SNPs is not equally among the chromosomes. These SNPs will be effective tools to facilitate genetic analysis on traits with economical interests and to overview the process of breeding among temperate Japonica cultivars.