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Gramene: Genetic Diversity Database

E.g., Germplasm "IRGC9542", RA4969, Basmati 1, Marker/locus RM22.
Check out our new tutorial videos! Gramene Diversity Overview, MLM Analysis with TASSEL

Focus of the Genetic Diversity module

Characterizing the genetic basis of variation in plants and linking to observable traits will provide an important framework for understanding population structure, evolutionary patterns, and could potentially significantly increase the efficiency of selections made in plant breeding programs. The Genetic Diversity module specializes in storage of genotypes, phenotypes and their environments, germplasm, and association data. We implement the Genomic Diversity and Phenotype Data Model (GDPDM) database schema, which efficiently stores anything from small-scale SSR diversity studies to large-scale SNP/indel-based genotype-phenotype studies with billions of allele calls.

Diversity Data Summary

Species New Data Set
Arabidopsis Atwell et. al, Nature June 2010. Genotype, phenotype, association data. ~214,000 SNPs, 199 Germplasm, 107 Phenotypes, TAIR10. [View]
New! Explore Atwell GWAS data in our Association Viewer (beta), TAIR 10
2010 Project SNP Discovery: 637,522 SNPs x 20 ecotypes, TAIR10. [View]
2010 Project 250K SNP chip genotypes v3.06, 214,052 SNPs x 1307 ecotypes, TAIR10. [View]
2010 Project 250K SNP chip genotypes v3.04, 214,545 SNPs x 1179 ecotypes, TAIR10. [View]
1001 Genomes/WTCHG SNPs from dbSNP, 2.7 million SNPs, 17 ecotypes, TAIR10. [View]
Rice * Zhao K, et al, Nat Comm, 2011. Rice GWAS study. 413 diverse accessions, Rice Diversity 44K SNP array, 34 phenotypes. MSU6 coordinates [View]
* Zhao K, et al, Nat Comm, 2011. Rice GWAS study. 413 diverse accessions, Rice Diversity 44K SNP array, 34 phenotypes. MSU7 coordinates [View]
Huang X, et al, Nat Genetics 2010 Nov. Rice HaplotypeMap GWAS study. 842,474 SNPs*, 374 landraces, 14 phenotypes. *IRGSP4 coordinates [View]
Zhao K, et al PLoS May 2010, Rice Diversity 1536 SNP array: 1311 SNPs x 395 varieties, mapped to MSU6. [View]
* Zhao K, et al PLoS May 2010, Rice Diversity 1536 SNP array: 1311 SNPs x 395 varieties, mapped to MSU7. [View]
MSU6, McNally et al. 2009, 160,000 SNPs x 21 varieties (incl. Nipponbare ref.) from OryzaSNP. [View]
* (G) Fan C, et al, Theor Appl Genet, 2009. C-A mutation in GS3 associated with grain length, phenotype study. 180 germplasm, trait: grain length [View]
* (G) Yoshida K, et al, Genes & genetic systems, 2009. DNA polymorphism in Pi-ta gene. 12 germplasm, trait: blast resistance [View]
* (G) Maas L, et al, Theor Appl Genet, 2010. Flowering time study. 19 germplasm, trait: days to flower, grain yield [View]
* (G) Wang X, et al, Phytopathology, 2008. Diversity study at Pi-ta locus. 47 germplasm, trait: blast disease [View]
* (G) Jia Y, et al, Pythopathology, 2003. Diversity study of Pi-ta locus. 9 germplasm, trait: blast disease [View]
* (G) Wei X, et al, Plant Physiol, 2010. Study of DTH8 supression of flowering time, plant height, yield potential. 40 germplasm, trait: days to heading [View]
* (G) Ebana K, et al, Theor Appl Genet, 2011. Heading date diversity study. 12 germplasm, trait: blast resistance [View]
* (G) Study of molecular evolution of shattering in U.S. weedy rice. 105 germplasm, trait: grain shattering [View]
* (G) Mao H, et al, Proc Natl Acad Sci USA, 2010. Grain size variation study. 82 germplasm, trait: grain length [View]
* (G) Jia Y, et al, Phytopathology, 2004. Pi-ta gene study. 20 germplasm, trait: blast disease [View]
(G) Wang X, et al, Plant Breeding, 2009. Pi-ta gene phenotype study. 194 germplasm, trait: blast resistance [View]
(G) Wang Z, et al, Plant Breeding, 2007. Pi-ta gene phenotype study. 138 germplasm, trait: blast resistance [View]
(G) Shomura et al, Nat Gen, 2008. Grain size phenotype study. 84 germplasm, traits: grain length, grain width, grain width-length ratio [View]
(G) Sweeney et al, PLoS Gen, 2007. Pericarp phenotype study. 440 germplasm, trait: pericarp color [View]
Gross B, et al, Mol Ecol, 2010. Rice grain color SNP diversity study on Chr 12, 633 SNPs x 143 rice accessions. [View]
Smaller scale, SSR, SNP, QTL diversity studies: Caicedo et al, 2007; Olsen et al, 2006; Garris et al, 2005; Lu et al, 2005; Semon et al, 2005; Jain et al, 2004; Thomson et al, 2003; Ramalingam et al, 2003; Ni et al, 2002; Xing et al, 2002; Moncada et al, 2001; Price A. et al, 2000; Maheswaran et al, 2000; G. Wang et al, 1994.
Maize Maize Diversity Hapmap1, AGPv2 coordinates, 1.6 million SNP x 27 NAM lines. [View]
Sorghum 6 datasets from Hamblin et. al. and the Sorghum Diversity Project which study variation using sequencing of direct PCR and SSRs [View]
Wheat SNP discovery data from the 'Haplotype polymorphism in polyploid wheats and their diploid ancestors' NSF project. [View]

(G) = Gene-based phenotype study.

SNP Data

SEARCH SNP data for overlapping genes, and filter by physical position or cultivar subsets with the SNP Query tool.

DOWNLOAD SNP data sets in the following formats: hapmap, plink, Flapjack. We encourage users to view these datasets in the Flapjack genotype viewer!

LAUNCH TASSEL with SNP data sets. View our TASSEL video demo!.

Germplasm Search

Search for experiments that contain a germplasm named

Also see our Germplasm module.



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