News
IRIC Under New Leadership
On February 5th, Dr. Rod Wing of the Arizona Genomics Institute was voted as the new Chair of IRIC by the Advisory Committee. He will be coordinating IRIC activities. Rod will help promote IRIC at different workshops and engage more people to be involved in the consortium. One focus will be raising additional funds for sustaining IRIC and further development of tools for the community. Under the new leadership, one of the goals for this year is integrating new platinum reference genomes into SNP-seek. In addition, fifteen high quality reference genomes representing each of the 15 subpopulations of the 3K genomes will be generated this year. |
Order seed through snp-seek
Ordering seed is made easier for breeders. You can now order seeds from the IRRI Genebank Collection through our Seed Ordering Page in snp-seek. Visit snp-seek for your orders. |
GWAS viewer
The GWAS module allows viewing and filtering of results from pre-computed analyses. The analyses presented are from phenotypic data on morphological and agronomic traits on the source accessions from which genetic stocks were derived and sequenced. A paper on the GWAS results is in preparation and nearing submission (Sangcianco et. al.). Visit snp-seek to learn more. |
3K RG 1M GWAS SNP Dataset available for download in SNP-Seek
New LD pruned subset to try for GWAS is available as downloadable dataset in snp-seek. The data is based on the Filtered SNP set (4.8M), a subset of Base SNP (18M). It was done with one round of LD pruning, r2 cutoff 0.8, window size 2kb and step 1 SNP, to remove only SNPs that are less than ~2kb apart. This leaves 1, 011, 601 snps. Visit our Bulk Download Page, scroll down and look for 3K RG 1M GWAS SNP Dataset, all chromosomes. ![]() |
Haplotype view available in SNP-Seek
A new feature in SNP-Seek that will make snp mining easier and more fun is made available. Haplotype view is here. Just visit snp-seek.irri.org and make a query in genotype search and choose the Haplotype view as shown below. The haplotype view allows user to cluster and visualize the genotype groups of varieties. |
Salinity phenotype data available in SNP-seek
Dr. RK Singh's team evaluated response to salinity stress measured for electrical conductivity at 12 dS/m and 18 dS/m during seedling stage for 1,999 genomes from 3Krg dataset. The data is labeled as “salt injury” in the SNP-seek database. |
SNP-Seek USE CASE: Get variations in a region
A. Given a region of interest (gene), get similar varieties Region of interest: LOC_Os04g57530
For more use cases visit our Help page. |
IRIC Workshop at PAG XXV
The IRIC Workshop will be held on 18 January 2017 at Plant and Animal Genome Conference XXV in San Diego, California. Talks will be given by Nickolai Alexandrov, David Edwards, Dario Copetti, Pierre Larmande, Tatiana Tatarinova and Jeremy Edwards. The talks are:
Locedie Mansueto, a developer from IRRI, will deliver a demonstration about the features of SNP-Seek on the same day at 11:00 a.m and present the scientific poster SNP-Seek Resource for Rice Research. |
IR8
As we celebrate the 50th anniversary of the official release of IR8, we are pleased to announce the availability of IR8's high quality genome assembly, using whole genome shotgun sequencing. The semidwarf rice variety is considered as miracle rice for it is believed to have saved Asia from famine during the late 1960s. |
New Feature released
Another feature has been added to further assist you in your snp-seeking. Searching across the 3K panel for similar accession to particular accession is now possible. Choose the accession of interest as reference for the rest of the 3k panel by choosing the Accession in the variety drop down menu in the Region section. Visit our online rice snp-seek database at http://snp-seek.irri.org. |