Introduction to the Gramene Genetic Diversity module

5/2010Build #31

• The Gramene Genetic Diversity database module specializes in storage of data sets that study genetic variation and genotype-phenotype association in populations of plants.

Rice

Maize

Arabidopsis

SorghumWheat

• Our focus: – Storage of large-scale SNP and

indel genotype datasets and accompanying phenotype measurements

– Facilitate discovery of associations between genes and traits

– Species of primary interest: maize, rice, Arabidopsis. We also house some important wheat and sorghum data

To find the Genetic Diversity module:- Go to: www.gramene.org, and click on one of the Diversity links

- Or, navigate go there directly: www.gramene.org.diversity

Click on “Diversity” thumbnail

Click on “Diversity”

link

What’s on the Diversity main pageBrowse data

Access latest Diversity datasets

Large-scale SNP datasets

Browse through SSR, RFLP and other smaller scale diversity or

QTL studies here

What’s on the Diversity main pageSearch data

Quick searchfor germplasm

or markersSNP QueryTool for miningSNP data

What’s on the Diversity main pageDownloading data

Download SNP data inhapmap, plink and flapjack format. Click on the DOWNLOAD link and we’ll take a look at the Download Data page on the

next slide…

Download subsets of SNP data by using the SNP Query tool (more

about this in a few slides)

Launch Diversity datasets live in

TASSEL. Download graphs and results

from analyses

All download options, including full Diversity

MySQL db dumps

• The large-scale SNP datasets are offered for download in hapmap, plink (.map and .ped files) and flapjack format. The plink files are loadable in the PLINK analysis program (pngu.mgh.harvard.edu/~purcell/plink) and the flapjack project files are loadable in Flapjack visualization tool (bioinf.scri.ac.uk/flapjack).

SNP download pagewww.gramene.org/diversity/download_data.html

Phenotype

Field/Plant information

Germplasm

Genotype

The Diversity module stores all of its data in MySQL using the GDPDM database model.

GDPDM links genotype, phenotype, germplasm, field and environment information in one resource.GDPDM v 4.0 is optimized for efficient handling of large scale SNP data by using BLOBs (binary database objects)

For full GDPDM documentation, go here: http://www.maizegenetics.net/gdpdm/documentation_list.html

SNP QUERYWeb-based tool for mining SNP datasets in Gramene Genetic Diversity

Features of the ‘SNP Data’ area of Diversity:SNP QUERY TOOL

Click SEARCH link to go to SNP Query

Select a species

Select a dataset to load

Select subset of plants in the

experiment by holding down the

SHIFT, ALT, or APPLE-CMD key while

clicking. The default (selecting none) will

return data for all accessions.

Select chromosome

Optionally enter start and stop coordinate for

range of interest

Select output format. ‘Text’ and ‘HTML’ will return the results in the browser, ‘File download’ will return results as a downloadable csv text

file.

Finally, click Submit

Here’s what the HTML results of SNP Query look like:

Hyperlinked to Gramene Genomes Ensembl browser

You can save the results to your hard disk as text

(some browsers allow you to save in HTML), or you can redo your query and

select File Download option

TASSELJava program for evaluating trait associations, evolutionary patterns,

and linkage disequilibrium

TASSELLaunch Diversity SNP datasets with Java web-start

Click on the LAUNCH TASSEL

link to access the web-start links

TASSELLaunch Diversity SNP datasets with Java web-start

www.gramene.org/diversity/tassel_launch.html

When you click on one of the hyperlinks, each of which represent one chromosome’s worth of SNP data, a dialog box

should appear asking you if you want to open Java Web Start to open the file – click OK. TASSEL will take a minute or two to

launch…

Once TASSEL launches, here is what you should see:

Notice the dataset tag ‘chr1’ appears in the

left bar. Click on ‘chr1’ to see the data….

When you click ‘chr1’ in left Data column, the data will be displayed in main window:

LD v DistanceDiversity

sliding windowPhylogeny LD

PCA of genotypes

With TASSEL you can perform many analyses. Please see TASSEL

documentation for much more information:

maizegenetics.net/tassel