IPK Gatersleben - BRIDGE Web Portal

Welcome to the IPK visual analytics tool suite for barley genebank genomics

Features

	Search more than 22,000 barley germplasm samples by passport and phenotypic data
	Visually explore hundreds of thousands of SNPs called against Morex V1, V2 and V3
	Visualize and select germplasm on the interactive world map
	Inspect genetic diversity via scatterplots of PCA and t-SNE dimensionality reduction
	Inspect GWAS results with interactive Manhattan plots
	Export of genotypic data in VCF files
	Export of phenotypic data in ISA-Tab format
	Order your barley accessions of interest directly from the IPK Genebank

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Recent updates

2021

07.06.2021: The legacy SNP-Browser for Morex V1 has been removed
02.06.2021: The layout of the startpage was renewed
30.04.2021: Added SNP-Browser for Morex V3 referenced genotype panel with all 22626 BRIDGE genotypes
30.04.2021: Added BLAST-feature to SNP-Browsers for Morex V2 and V3

2020

15.11.2020: Added SNP-Browser for Morex V2 referenced genotype panel with all 22626 BRIDGE genotypes
15.11.2020: Major update of the SNP-Browser with new features: Display of SnpEff annotations, Local PCA, Display of per-SNP-metadata
25.02.2020: Added DOIs of germplasm origin genebank accession and descendant material (where available)
03.02.2020: Fixed bug in VCF export service

2019

07.11.2019: New feature added: new buttons in "Select Germplasm" page for filter search result by "Only germplasm with a photo" and "Only germplasm with phenotypic data"
05.11.2019: New feature added: MIAPPE-compliant ISA-Tab export of phenotypic data
17.07.2019: New feature added: "Genetic Distance Color Mapper" to colorize scatterplots by genetic distance to the reference genotype
10.07.2019: New feature added: "Phenotype Data Color Mapper" to map phenotypic traits on scatterplots and the worldmap
24.06.2019: Added column in germplasm search result table to show if phenotypic data is available for a germpplasm sample
20.06.2019: Added possibility to search for specific accession number prefixes on "Search Germplasm" page

2018

15.11.2018: Added a page "Germplasm collections" where one can see created collections in a datatables.
06.09.2018: Added a page "Germplasm details" where one can see passport data and phenotypic data of accessions.
10.04.2018: Added possibility to load core 1000, core 200 and core 50 set of accessions (in the tab "Select Germplasm")
29.03.2018: In addition to the unimputed SNP matrix, the imputed SNP matrix (basis for the GWAS) has also been added to the SNP Browser
27.03.2018: SNP Browser was improved with functionality to filter SNP's by either minor allele frequency, minor allele count, fraction of heterozygosity and/or fraction of missing calls
09.03.2018: In the "Manage your filters"-dialogue the defined filter sets can now be saved as a file and loaded again. With this feature a user can send his filter sets to a associates via E-Mail for collaborate work.
02.03.2018: New feature added: Link between GWAS plot and SNP Browser (click on a SNP position in GWAS-plot and you get the corresponding position in the SNP Browser on your screen)
22.02.2018: New feature added: PCA Scatterplot Matrix in the tab "PCA Matrix"

2017

08.11.2017: Added "Institute Code" and "Donor Institute Code" in filter result datatable with links to www.fao.org
02.11.2017: Added new tab with a parallel coordinate plot of the first ten principle components
27.10.2017: A photo of the accession (if available) is now displayed as a tooltip when hovering over the Photo-link in the filter result datatable
26.10.2017: Ability to switch off spike and grain filter panel; filtered accessions are now displayed in a datatable below filter panels
20.10.2017: New tab "Statistics" with world map to visualize the number of accessions per country
17.10.2017: Possibility to change dot transparency in PCA plots with a slider for each named filter set
16.10.2017: Possibility to change filter set color afterwards by clicking on the appropriate color swatch in the modal dialog that opens after click on "Show list of filters"-button

Data summary

22,626 barley germplasm samples
9,527 samples with phenotypic data
6,162 samples with a spike photo
2,862 samples with geographic coordinates
15 phenotypic traits of spike, awn and seeds
5 traits as GWAS results

Available SNP sets as SNP-Browser:

Reference genome	# SNPs	# Genes
Morex V1	171,263	39,734
Morex V2	775,283	63,658
Morex V3	1,052,403	81,687

How to cite

Citations keep this service running. If you use BRIDGE please cite:

König P, Beier S, Basterrechea M, Schüler D, Arend D, Mascher M, Stein N, Scholz U and Lange M. BRIDGE - A Visual Analytics Web Tool for Barley Genebank Genomics. Frontiers in Plant Science (2020) doi.org/10.3389/fpls.2020.00701

References

Milner, S.G., Jost, M., Taketa, S. et al. Genebank genomics highlights the diversity of a global barley collection. Nat Genet 51, 319–326 (2019). doi.org/10.1038/s41588-018-0266-x

Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, Pozniak CJ, Sharpe AG, Simková H, Moscou MJ, Grimwood J, Schmutz J, Stein N. Long-read sequence assembly: a technical evaluation in barley. The Plant Cell (2021). doi.org/10.1093/plcell/koab077

Monat, C., Padmarasu, S., Lux, T. et al. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 20, 284 (2019). doi.org/10.1186/s13059-019-1899-5

Mascher, M., Gundlach, H., Himmelbach, A. et al. A chromosome conformation capture ordered sequence of the barley genome. Nature 544, 427–433 (2017). doi.org/10.1038/nature22043

Beier, S., Himmelbach, A., Colmsee, C. et al. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.. Sci Data 4, 170044 (2017). doi.org/10.1038/sdata.2017.44

General Filter

Passport attributes

Country of origin

Annuality

Row type

Subspecies

Status

Collection site

Donor institute

Only germplasm with a photo

Only germplasm with phenotypic data

Other attributes

Part of core collection*

Accession number prefix

* as descibed in Milner et al. (2019)

Phenotypic Trait Filter

Spike

Row-Type-Convarity

Spike density

Spike branching

Spike brittleness

Awns

Awns roughness

Awns central spikelets

Awns lateral spikelets

Awns on glumes

Grain

Grain hull / Cover of caryopses

Color of naked seeds

Rachilla hairs

Glume

Glume width

Color of glumes

Accession Number Filter

Insert a comma separated list of accession numbers e.g. "HOR 1, HOR 2"

Search result

germplasm samples were found with your given search criterions.

Loading tabular data...

Morex V3
Morex V2
Morex V1

No accessions selected.

Dot colors:

Dot size:

Dataset:

X axis:

Y axis:

Invert: X axis Y axis

Explained variance per principle component:

PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10
2.46 %	2.36 %	1.26 %	0.88 %	0.81 %	0.66 %	0.60 %	0.52 %	0.50 %	0.41 %

Explained variance per principle component:

PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10
11.91 %	8.89 %	6.13 %	2.65 %	2.16 %	2.03 %	1.74 %	1.34 %	1.14 %	0.99 %

Explained variance per principle component:

PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10
10.45 %	9.72 %	4.98 %	2.75 %	2.47 %	1.99 %	1.69 %	1.54 %	1.06 %	0.99 %

Transparency adjustment sliders:

Interactive worldmap: Clicking on a country highlights the corresponding samples in the scatterplot on the left. By holding down the Shift-key while clicking you can select multiple countries at once.

Dataset:

Transparency adjustment sliders:

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Pheno parallelplot

Trait:

By clicking on a point in the plot you will be directly redirected to the corresponding position in the SNP Browser.

All GWAS calculations are based on SNPs called to the Morex v1 reference genome.

Subpopulation A:

Subpopulation B:

VCF Export of genotypic data

The VCF Export feature has been refactored. Please use the button "VCF Export" in the SNP Browser to export VCF files of different Morex versions.

Germplasm details

Passport data Phenotypic data Photo

Passport data at project start

Important hint: The following passport data reflects the state of data at the beginning of the project, which was also the basis for data analyses such as GWAS and genetic clustering. Passport data is mutable and can change due to the data curation of the responsible genebank during the course of the project or after the end of the project. Changes in the passport data that occurred afterwards are listed in the area one below with the title "Passport data changelog".

Passport data changelog

Phenotypic data

Photo

You have not selected an accession. Please use the "Select Germplasm" link on the left hand side to search for one or more accessions and then click on the "Details" link in the search results table.

Saved germplasm collections

Predefined collections:

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