Plasmids were isolated using the DNA-spin Plasmid DNA Purification Kit (Intron Biotechnology, Korea) and sequenced with an ABI-3700 DNA sequencer following the manufacturer’s instructions(Applied Biosystems, Inc.).
To identify SNPs, insertions and deletions(Indels), and/or microsatellite repeats in the rice varieties, sequence results were aligned using the CLUSTAL W program (22) from EMBLEuropean Bioinformatics Institute (http://www.ebi.ac.uk/tools), with assistance from Codoncode Aligner 2.0.6 (CodonCode Corporation,Dedham, MA) as well as BioEdit (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).