Data Sets


Population Structure in the Oryza rufipogon Species Complex

Kim H, Jung J, Singh N, Greenberg A, Doyle J, Tyagi W, Chung J-W, Kimball J, Hamilton R, McCouch S (2016) Population dynamics among six major groups of the Oryza rufipogon species complex, wild relative of cultivated Asian rice. Rice 9:56 doi 10.1186/s12284-016-0119-0

• Germplasm

• Genotypes

  • Nuclear GBS data: NCBI batch submission ID is 1062455 (Link)
  • Chloroplast SNP data: the accession for each region listed below. The records can be retrieved from the nucleotide database by searching Entrez Nucleotide: Using the accession numbers.
    • chloroplast_region1: KX556608 - KX556920
    • chloroplast_region2: KX556921 - KX557233
    • chloroplast_region3: KX556295 - KX556607
    • chloroplast_region4: KX555982 - KX556294
    • chloroplast_region5: KX555669 - KX555981

High Density Rice Array (HDRA, 700k SNPs)

McCouch S, Wright M, Tung C-W, Maron L, McNally K, Fitzgerald M, Singh N, DeClerck G, Agosto Perez F, Korniliev P, Greenberg A, Nareda ME, Mercado SM, Harrington S, Shi Y, Branchini D, Kuser-Falçao, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J. (2016) Open Access Resources for Genome Wide Association Mapping in Rice. Nature Comm, 7: 10532 doi 10.1038/ncomms10532

• Germplasm

• Genotypes

• Phenotypes

• GWAS Results

All GWAS results were generated by using our GWAS pipeline which can be obtained from our Tools and Resources section

•NCBI Assets


Panicle Architecture

Crowell S, Korniliev P, Falcão A, Ismail A, Gregorio G, Mezey J, McCouch S. 2016. Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters. Nature Communications (in press).

Genomic Selection for IRRI breeding population