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Nucleic Acids Res. 2015 Jan;43(Database issue):D1023-7. doi: 10.1093/nar/gku1039. Epub 2014 Nov 27.

SNP-Seek database of SNPs derived from 3000 rice genomes.

Author information

1
T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.
2
BGI, Shenzhen 518083, China.
3
Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081.
4
T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines.
5
BGI, Shenzhen 518083, China zhanggengyun@genomics.cn.
6
Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 lizhikang@caas.cn.

Abstract

We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.

PMID:
25429973
PMCID:
PMC4383887
DOI:
10.1093/nar/gku1039
[Indexed for MEDLINE]
Free PMC Article

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