Data Sets

C7AIR – 7K SNP array

Morales KY, Singh N, Perez FA, Ignacio JC, Thapa R, Arbelaez JD, et al. (2020) An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies. PLoS ONE 15(5): e0232479. [Paper download] ">

• Germplasm

  • S1 Table. List of 544 Oryza accessions with inferred ancestry and subpopulation assignments [Excel File]

• SNP data

  • S2 Table. Trait-specific SNP markers [Excel File]
  • S3 Table. SNP Manifest File [Excel File]
  • S4 Table. SNP Genotype Data Matrix for 7,098 SNPs x 544 Oryza accessions and plant height data for subset of accessions [Excel File]

• Kinship Values

  • S5 Table. Kinship values generated using highest performing SNPs [Excel File]

• Polymorphism comparisons

  • S6 Table. Polymorphisms between and within Oryza species, subpopulations [Excel File]

Rice Imputation

Diane R. Wang, Francisco Agosto-Perez, Dmytro Chebotarov, Yuxin Shi, Jonathan Marchini, Melissa Fitzgerald, Kenneth L. McNally, Nickolai Alexandrov, Susan R. McCouch. An imputation platform to enable efficient integration of rice genetic resources. Nature Communications doi 10.1038/s41467-018-05538-1

• Genotypes

• Data for indica GWA using imputed data

• GWA Results

CSSLs for Curinga x O. meridionalis and Curinga x O. rufipogon

Arbelaez JD, Moreno LT, Singh N, Tung CW, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch SR (2015) Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. Mol Breeding 35:81. doi 10.1007/s11032-015-0276-7

• Germplasm

• Genotypes

  • Combined GBS and 6K Minimun SNP set
  • Other tables, figures and supplementary materials

  • 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