title: Development of genome-wide DNA polymorphism database for map-based cloning of rice genes.
abstract: DNA polymorphism is the basis to develop molecular markers that are widely used in genetic mapping today. A genome-wide rice (Oryza sativa) DNA polymorphism database has been constructed in this work using the genomes of Nipponbare, a cultivar of japonica, and 93-11, a cultivar of indica. This database contains 1,703,176 single nucleotide polymorphisms (SNPs) and 479,406 Insertion/Deletions (InDels), approximately one SNP every 268 bp and one InDel every 953 bp in rice genome. Both SNPs and InDels in the database were experimentally validated. Of 109 randomly selected SNPs, 107 SNPs (98.2%) are accurate. PCR analysis indicated that 90% (97 of 108) of InDels in the database could be used as molecular markers, and 68% to 89% of the 97 InDel markers have polymorphisms between other indica cultivars (Guang-lu-ai 4 and Long-te-pu B) and japonica cultivars (Zhong-hua 11 and 9522). This suggests that this database can be used not only for Nipponbare and 93-11, but also for other japonica and indica cultivars. While validating InDel polymorphisms in the database, a set of InDel markers with each chromosome 3 to 5 marker was developed. These markers are inexpensive and easy to use, and can be used for any combination of japonica and indica cultivars used in this work. This rice DNA polymorphism database will be a valuable resource and important tool for map-based cloning of rice gene, as well as in other various research on rice (http://shenghuan.shnu.edu.cn/ricemarker).
authors.affiliation: College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
authors.forename: Ying-Jia
authors.initials: YJ
authors.lastname: Shen
authors.forename: Hua
authors.initials: H
authors.lastname: Jiang
authors.forename: Jian-Peng
authors.initials: JP
authors.lastname: Jin
authors.forename: Zai-Bao
authors.initials: ZB
authors.lastname: Zhang
authors.forename: Biao
authors.initials: B
authors.lastname: Xi
authors.forename: You-Yu
authors.initials: YY
authors.lastname: He
authors.forename: Guan
authors.initials: G
authors.lastname: Wang
authors.forename: Chen
authors.initials: C
authors.lastname: Wang
authors.forename: Lily
authors.initials: L
authors.lastname: Qian
authors.forename: Xiang
authors.initials: X
authors.lastname: Li
authors.forename: Qing-Bo
authors.initials: QB
authors.lastname: Yu
authors.forename: Hui-Juan
authors.initials: HJ
authors.lastname: Liu
authors.forename: De-Hui
authors.initials: DH
authors.lastname: Chen
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Gao
authors.forename: Hai
authors.initials: H
authors.lastname: Huang
authors.forename: Tie-Liu
authors.initials: TL
authors.lastname: Shi
authors.forename: Zhong-Nan
authors.initials: ZN
authors.lastname: Yang
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D018744:DNA, Plant / Q000235:genetics*; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D018744:DNA, Plant