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.

 Table. Brief descriptions of data and tools to be initially available for IRIC members in 2016

 Materials /data / tools
  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.
  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