SNP-Seek database of SNPs derived from 3000 rice genomes

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.

Figure 1.

Basic schema of the SNP-Seek database

Figure 2.

Distribution of SNP coverage

Figure 3.

SNP distribution by varieties. The major peak shows that about 14 M SNPs have been called in most varieties. The bimodal plot indicates that a fraction of SNPs are missing in some varieties, likely due to lack of mapped reads in variable regions.

Figure 4.

Multidimensional scaling plot of the 3000 rice varieties. Ind1, ind2 and ind3 are three groups of indica rice, indx corresponds to other indica varieties, temp is temperate japonica, trop is tropical japonica, temp/trop and trop/temp are admixed temperate and tropical japonica varieties, japx is other japonica varieties, aus is aus, inax is admixed aus and indica, aro is aromatic and admix is all other unassigned varieties.

Figure 5.

Jbrowse view of the SNP genotypes within the sd-1 gene (each variety is one row). Red blocks indicate polymorphism of the variety against Nipponbare. Shared SNP blocks are seen as vertical columns in red. The blue rectangle box in the bottom contains varieties that do not have these blocks.