Development of genome-wide DNA polymorphism database for map-based cloning of rice genes.
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).
Shen
Ying-Jia
YJ
College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
Jiang
Hua
H
Jin
Jian-Peng
JP
Zhang
Zai-Bao
ZB
Xi
Biao
B
He
You-Yu
YY
Wang
Guan
G
Wang
Chen
C
Qian
Lily
L
Li
Xiang
X
Yu
Qing-Bo
QB
Liu
Hui-Juan
HJ
Chen
De-Hui
DH
Gao
Jian-Hua
JH
Huang
Hai
H
Shi
Tie-Liu
TL
Yang
Zhong-Nan
ZN
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
D018744:DNA, Plant