Projects
Initial datasets and tools provided
The datasets listed below will be organized into an initial, curated IRIC database with proper constraints and indices. The access to this data will be provided via a user-friendly web portal enabling basic search, browsing and simple trait-phenotype association analysis. More genotyping and phenotyping data obtained through research conducted by IRIC members will be added as they become available, subject to conditions imposed by the owners of the data. Additional web-based applications for more types of low-throughput statistical analysis and data manipulation will also be available soon.
Brief descriptions of data and tools to be initially available for IRIC members in 2016
IRRI Genebank genetic stocks for trait discovery research
~4500 lines with standard unique name and origins
Purified seed of all lines can be requested via IRRI seed request forms, subject to standard handling and shipping charges.
Some are also available through the USDA’s Genetic Stocks Oryza collection in Stuttgart USA
Genotypic data
~40M SNPs from about ~3000 rice genomes (BGI/ CAAS/IRRI)
~700K SNP chip for ~1800 lines (Cornell/USDA/NSF/IRRI)
~44K SNP chip for ~400 lines (Cornell/USDA/NSF)
~18M SNPs from 54 elite cultivars from US and CIAT rice breeding programs (Duitama, Tohme et al 2015)
All SNPs will be mapped into annotated genome assemblies
Os-Nipponbare-Reference-IRGSP-1.0 japonica assembly with MSU7/RAP annotations
BGI newest assembly of indica 93-11. Annotation to be determined or provided
Draft genome assemblies of indica (IR64 - Cold Spring Harbor/Cornell, 93-11 - BGI), and aus (DJ123 - Cold Spring Harbor/Cornell, Kasalath - NIAS , Japan)
Phenotypic data
~60 morphological traits observed for genetic stock lines from the IRRI Genebank
~30 traits for ~400 lines genotyped with 44K & 700K SNPs (from USDA Stuttgart)
~60 traits for ~350 indica lines genotyped with 700K chip (Global Rice Phenotyping Network)
grain quality traits ~1600 lines genotyped with 700K chip for
~25 traits for ~300 tropical japonica and ~250 aus lines genotyped with 700K chip
Gene expression data
Basic developmental and selected stress experiments from NIAS, Japan
RNA-Seq data from C4 consortium