Rice (Oryza sativa L.) is one of the significant cereal crops feeding a large number of worldwide populations. It is also one of the well-studied model organisms for plant research. Due to increasingly adverse environmental conditions and scarce natural resources, the need to breed robust and high-productivity rice varieties is more important than ever. Rice yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Rice breeders try to protect yield losses from environmental stresses by incorporating resistance genes and developing more climatically resilient cultivars. Thus, it is of great importance to perform in-depth explorations on the genes that are closely associated with these important agronomic traits.

Rice Stress-Resistant SNP Database includes the following data:

  1. Basic information of the 400 rice stress-resistant accessions, including accession names, and meta-information such as geological locations, subspecies (or subgroups) categorizations and stress responsiveness of each variety.
  2. The annotation of 9.9 million SNPs specific to resistance resistant varieties, including the statistical information overall SNPs in each stress-resistant subgroups.
  3. The presence or absence of each SNP in each stress-resistant variety, Including the annotation and description of each gene.

How to use Rice Stress-Resistant SNP Database

Browse Varieties

Rice Stress-Resistant SNP Database database summarizes the stress-resistant varieties by phenotype. Select the stress type, it will list all the varieties resistant resistant to the selected phenotype, it will display the metadata of each variety including the stress resistance responsiveness of each variety as Resistant(R), Moderately Resistant(MR) and Highly Resistant(HR).

Browse Varieties

Figure 1: Browse varieties Interface.

Browse SNPs

Rice Stress-Resistant SNP Database summarizes SNP number by chromosome of each phenotype subgroup. In addition it provides the SNP summary of each variety in each sub group.

Browse Varieties

Figure 2: Browse SNPs Interface

Browse Varieties

Figure 3: Total Distribution of SNPs in each phenotype selected.

Browse Varieties

Search SNP

Main search functions:

  1. Search SNPs by genome position
  2. Search SNPs by gene ID) to obtain its basic information, distributions, PAVs and gene functions.
  3. Search SNP by SNPID.
  4. Set options(select variant type or maf(minor allele frequency)).
Browse Varieties
Browse Varieties

Figure 4: Search SNP Interface

Search by Genome Position

  1. Must select phenotype.
  2. Must choose chromosome , start and end positions
  3. Optional, set variant type and minor allele frequency of interest
Browse Varieties

Figure 5: Search by genome position.

Search SNPs by gene ID

  1. Must select phenotype.
  2. Must enter gene ID (eg. Os01g0117300).
  3. Optional, set variant type and minor allele frequency of interest.
Browse Varieties

Figure 6: Search by GeneID

Search SNPs by SNP ID

  1. Must select phenotype
  2. Must enter SNP ID: The SNP ID has this format SNPCHXXXXXXXX and it is composed of the prefix SNP for the variant type, CH represents the chromosome number, 01,02,03,04,05,06,07,08,09,10,11,12 and the last 8 X values represent the chromosome coordinate, eg SNP at chromosome chr01, Position 1203, its ID is SNP0100001203.
  3. Optional, set variant type and minor allele frequency of interest.
Browse Varieties

Figure 7: Search by SNP ID position.

Search Results

The search results includes two output format, Tabular view displays:

  1. SNP ID
  2. Chrom
  3. Position
  4. Allels
  5. Gene ID
  6. Variant Annotation
Browse Varieties

Figure 8: SNP search results tabular view.

The graphical view presents the allele frequency distribution in the selected genome coordinate.

Browse Varieties

Figure 9: Allele frequency distribution view.

View SNP Detail

The SNP detail view has two parts the first part shows the detail of each SNP including the annotation, the genotype and the associated gene detail and annotation. The second part is the data visualization of the SNPs. This part has the feature to select different tracks of different stress type variants and gene/transcripts tracks. The detail of each SNP can be expanded by clicking at each SNP ID.

Browse Varieties
Browse Varieties

Figure 10: SNP Detail view.

Genome Browser view

The visualization page displays the SNPs and the alignment of each stress-variant tracks, genes and transcript tracks. The detail of each SNP and its annotation is also displayed.

Browse Varieties
Browse Varieties

Database design layout

Browse Varieties

Variant detection pipeline