1 / 23

Gramene Genetic Diversity and Variation

Gramene Genetic Diversity and Variation. Doreen Ware USDA ARS And Cold Spring Harbor Laboratory. Exploring Genetic Diversity. Visualization within genome context Consequence prediction gene structure/function Genotype/germplasm data Ensembl variation database. browser.

bran
Download Presentation

Gramene Genetic Diversity and Variation

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. GrameneGenetic Diversity and Variation Doreen Ware USDA ARS And Cold Spring Harbor Laboratory

  2. Exploring Genetic Diversity • Visualization within genome context • Consequence prediction gene structure/function • Genotype/germplasm data • Ensembl variation database browser Paul Kersey, Paul Derwent :EBI • Coordinate and gene-based SNP searches • Overlapping genome features • Bulk-download of SNP data in the HAPMAP and other standards • TASSEL launch: tool for LD and GWAS studies • Germplasm data and search • GDPDM database

  3. Browser Diversity Tracks

  4. Get On-Screen Details

  5. ResequencingView

  6. Gene Variation Image Shows functional consequence relative to gene and protein domain structure

  7. Gene Variation Table List by consequence type

  8. Protein-based SNP Annotation Highlights Variations that affect codons

  9. Graphical Genotype Comparison of Ecotypes

  10. Tabular Genotype Comparison of Ecotypes

  11. Variation Page Shows context within gene of interest and surrounding genes

  12. Population Allele Frequencies

  13. Identify Ecotypes Having Variant Allele Links to TAIR seed stock order form

  14. Genetic Diversity ModuleGDPDM data types • Associations • GWAS result • p-value, bpp, effect • Genotype • SNP, indel, GBS • supports full range of ploidy • connects to genomic map • Observed Plant • planting information • treatment • geographic data • individual plant sample • Germplasm • passport, stock tracking • source information • basic pedigree management • Phenotype • trait measurements • ontology terms • Genotype • captures wide range of approaches • supports full range of ploidy • connects to genomic map • Genotype • captures wide range of approaches • supports full range of ploidy • connects to genomic map • Genotype • captures wide range of approaches • supports full range of ploidy • connects to genomic map • Field/Plant Observation • integrates planting, treatment, locality data • field design links to individual plant sample • Field/Plant Observation • integrates planting, treatment, locality data • field design links to individual plant sample • Field/Plant Observation • integrates planting, treatment, locality data • field design links to individual plant sample • Germplasm • pedigree description • seed stock information • Germplasm • pedigree description • seed stock information • Germplasm • pedigree description • seed stock information • Phenotype • quantitative or qualitative traits • supports ontology integration • Phenotype • quantitative or qualitative traits • supports ontology integration • Phenotype • quantitative or qualitative traits • supports ontology integration

  15. Gramene Genetic Diversitywww.gramene.org/diversity

  16. SNP Query TASSEL 3.0 querying analysis Flapjack (SCRI) visualization

  17. Diversity Tools: SNP Query

  18. Diversity Downloads

  19. Diversity Downloads

  20. FlapjackScottish Crops Research Institute (SCRI)http://bioinf.scri.ac.uk/flapjack • Java stand-alone application • genotype and haplotype visualization in genomic and phenotypic context • Gramene collaborating with SCRI to streamline connectivity between TASSEL and Flapjack

  21. Diversity Tools: TASSEL

  22. Diversity Tools: TASSEL

  23. TASSELanalysis LD PCA of genotypes Manhattan Plot Phylogeny LD v Distance

More Related