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IRIC Under New Leadership

posted Mar 22, 2018, 4:53 PM by Frances Nikki Borja ‎(IRRI)‎

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.

Lastly, on behalf of the advisory committee and IRIC community, let us all thank Nickolai Alexandrov for his thoughtful leadership since the launch of IRIC.  We wish him all of the best in his new position in the USA.

Order seed through snp-seek

posted Jan 15, 2018, 5:11 PM by Frances Nikki Borja ‎(IRRI)‎

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

posted Jan 14, 2018, 5:49 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Jan 15, 2018, 3:52 PM ]

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

posted Oct 23, 2017, 8:09 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Oct 23, 2017, 11:19 PM ]

    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

posted Jul 31, 2017, 7:38 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Aug 1, 2017, 12:50 AM ]

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

posted Jul 9, 2017, 8:03 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Jul 9, 2017, 8:47 PM ]

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

posted Apr 6, 2017, 1:39 AM by Frances Nikki Borja ‎(IRRI)‎

A. Given a region of interest (gene), get similar varieties


Region of interest: LOC_Os04g57530


  1. Go to Genotype search page


  2. Supply the known information. Choose all varieties in the multiple: Subpopulation drop down menu in the Compare Varieties section. Supply the gene locus id in the Gene locus query box in the Region section.





  3. The table matrix showing the accession with variation in the region will be returned. There are 78 varieties that shown variation in this region. The table matrix is downloaded in CSV to further examine the region.



  4. Results can be downloaded as CSV format by clicking the CSV box in the Download section.




For more use cases visit our Help page.

IRIC Workshop at PAG XXV

posted Jan 4, 2017, 7:29 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Jan 5, 2017, 5:10 PM ]

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:

International Rice Informatics Consortium: 3,000 Rice Genomes Explorations and Beyond

Nickolai Alexandrov, International Rice Research Institute, Los Baños, Philippines

Development of WheatIS and Collaboration between Plant Information System

Chon-Kit Kenneth Chan1, Philipp E. Bayer1, Robert P. Davey2, Michael Alaux3, Cyril Pommier3, Hadi Quesneville3, Mario J Caccamo4, Gerard R. Lazo5, Kenneth L. McNally6, Nickolai Alexandrov6 and David Edwards1, (1)University of Western Australia, Perth, Australia, (2)Earlham Institute, Norwich, United Kingdom, (3)INRA - URGI, Versailles, France, (4)NIAB, Cambridge, United Kingdom, (5)USDA Agricultural Research Service, WRRC, Albany, CA, (6)International Rice Research Institute, Los Baños, Philippines

Development of Gap-Free Genome Assemblies to Capture and Exploit Rice Genetic Variation

Dario Copetti1, David Kudrna1, Jianwei Zhang1, Kenneth L. McNally2, Nickolai Alexandrov2, Ramil P. Mauleon2 and Rod Wing3, (1)Arizona Genomics Institute, Tucson, AZ, (2)International Rice Research Institute, Los Baños, Philippines, (3)School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, AZ

The Rice Data Interoperability Working Group

Pierre Larmande, IRD, UMR DIADE, Institut de Biologie Computationnelle, Montpellier, France, Ramil P. Mauleon, International Rice Research Institute, Los Baños, Philippines, Shaik N.M. N.Meera, Indian Institute of Rice Research (IIRR), Hyderabad, India, Imma S. Subirats, FAO, Rome, Italy and Devika M. Madalli, Indian Statistical Institute, Kolkata, India

Genome-Wide Analysis of SNPs in Promoter Regsions of Oryza sativa

Tatiana Tatarinova1, Victor Solovyev2, Kenneth L. McNally3 and Nickolai Alexandrov3, (1)University of Southern California, Los Angeles, CA, (2)Softberry, Mount Kisco, NY, (3)International Rice Research Institute, Los Baños, Philippines

Ricebase - a Resource for Rice Breeding

Jeremy D. Edwards, USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR

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

posted Dec 21, 2016, 7:57 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Dec 21, 2016, 10:43 PM ]

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.

The IR8 sequence and assembly are available at NCBI.

You can read more about IR8, its conception, history and many more at irri website.

New Feature released

posted Nov 9, 2016, 9:16 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Nov 9, 2016, 9:18 PM ]

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.



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