| DNA polymorphism is the basis to develop molecular markers that are widelyused in genetic mapping today. A genome-wide rice DNA polymorphism database hasbeen constructed in this work using the genomes of Nipponbare, a cultivar of japonica,and 93-11, a cultivar of indica. First, Contigs of 93-11 are used as queries to searchhomological sequences in Nipponbare by BLASTN. Then MUMmer3.0 and a seriesof VB scripts are used to detect the polymorphisms between homological sequencesof Nipponbare and 93-11 and construct the primary database. DNA polymorphismdatabase in rice is finally finished after filtering the less reliable polymorphisms andsorting the order of polymorphisms according to their positions on the chromosomes.This database contains 1,703,176 single nucleotide polymorphisms (SNPs) and479,406 Insertion/Deletions (InDels), approximately one SNP every 268 bp and oneInDel every 953 bp in rice genome. Both SNPs and InDels in the database wereexperimentally validated. Of 109 randomly selected SNPs, 107 SNPs (98.2%) areaccurate. PCR analysis indicated that 90% (97) of 108 InDels in the database could beused as molecular markers and 68-89% of the 97 InDel markers have polymorphismsbetween other indica cultivars (Guang-lu-ai 4 and Long-te-pu B) and japonicacultivars (Zhong-hua 11 and 95-22). This suggests that this database can be used notonly for Nipponbare and 93-11, but also for other japonica and indica cultivars. Whilevalidating InDel polymorphisms in the database, a set of InDel markers with eachchromosome 3-5 markers was developed. These markers are inexpensive and easy touse, and can be used for any combinations of japonica and indica cultivars used in thiswork. This rice DNA polymorphism database will be a valuable resource andimportant tool for map-based cloning of rice gene, as well as in other variousresearches on rice. (http://shenghuan.shnu.edu.cn/ricemarker)...
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