Resequencing Japonica rice 9522 variety, Oryza sativa, using Ion PGMTM Sequencer

The rapid development of the Next Generation Sequencing technology allows researchers to generate large amount of sequencing data at a very lost cost. Researchers now can resequence crop genomes with reference genomes to discover the SNPs and other mutations which are associated to important traits. In this project, wild-type rice cultivar 9522, Oryza sativa, was sequenced at 20x coverage using Ion 318^TM Chips on Ion PGM^TM System to study rice flower development. 11.2 Gb sequencing data was generated, of which 8.9 Gb data was ≥Q20 (99% accuracy).  95% of all reads were successfully mapped to the reference genome (http://rice.plantbiology.msu.edu/) for the downstream mutation analysis.  The deep sequencing results were used to identify SNP mutations and small indels. 30-50 detected mutations were randomly selected and validated by the capillary electrophoresis based sequencing. The sequencing efficiency and positive and negative detection rates of the Ion Semiconductor Sequencing System were evaluated.