1. Updates to the CSFL Genome Database:
Resources for pea, lentil, faba bean and chickpea genetics, genomics and breeding
Sook Jung, Jodi L. Humann, Chun-Huai Cheng, Taein Lee, Ping Zheng, Morgan Frank, Deah McGaughey, Kristin Scott, Katheryn Buble, Jing Yu, Heidi Hough, Clare Coyne, Rebecca McGee, Dorrie Main

2. Why CSFL?
A one-stop resource for genetic, genomics and breeding information about pea, lentil, chickpea and faba bean
Common tools pre-configured/pre- loaded for use with pea, lentil, chickpea and faba bean
Easy-to-use interfaces that allow quick access to the data and tools

3. What does CSFL have? Available Resources Pea Lentil Chickpea Faba Bean
Markers
7,041
50,058
54,442
3,431
Genetic Maps (CMap) 28 18 42 17
QTLs
820
150
514
210
Genomes 3
Searchable Sequences
Pea
Lentil
Chickpea
Faba Bean
RefTrans
Yes
Unigenes from ESTs No
ESTs
Genomes

4. CSFL Homepage

5. Crop Overview Pages

6. Data Searches

7. Data Searches

8. Available Tools

9. BLAST

10. BLAST

11. JBrowse
Open genomes by clicking on names on JBrowse page or by using “Genome” menu within JBrowse.

12. PathwayCyc
Pathway Tools analysis of C. arietinum CDC Frontier and C. reticulatum PI genomes
C. arietinum ICC 4958 in progress and will be available soon

13. MapViewer MapViewer will eventually replace CMap on CSFL
Similar to CMap, but uses the Chado data already in database
Access MapViewer from “Tools” menu or any genetic map details page
Comparative functions coming soon
MapViewer is a web based genetic map visualization tool that uses the D3 Javascript technology. It allows viewing of genetic maps and will show comparison of genetic maps that share the same markers, across the same or different species.
It is similar in functionality to the existing CMap genetic map comparison tool but offers the benefit of using map data directly stored in Chado, a generic database schema.
Sites that have both Chado and CMap can reduce their data duplication by using MapViewer because unlike CMap it requires no separate underlying database.

14. MapViewer
Can get to maps by clicking “view map” or click the LG

15. MapViewer – Zoom and Pan
The zoomed region on the right can be changed by clicking and dragging or changing the size of the window on the left
You can also see that panning on the left will cause the region to be shifted on the right.

16. MapViewer – Control Panel
Change linkage groups/maps
Change marker colors and which markers are visible
Hide/show ruler and marker positions
Here in the Control Panel, located below the linkage group view, you can change the linkage group, marker color and marker visibility

17. MapViewer – Comparisons
Coming in early 2018!
Can see corresponding markers in both maps and zoom and pan on each map individually

18. Breeders Information Management System (BIMS)
Breeding data fully integrated with data in database
CSFL continuously updated with genomic data, QTL data, publicly available cultivar evaluation data and molecular genotypic data
New and better marker development
Compare trait data between private germplasm and publically available germplasm
Components of BIMS
Archive
Manage Breeding
Data Import, Edit and Download
Search and Compare
Field Book App Management
Data Analysis Tools
Breeding Decision Tools

19. Data Import from Templates or FieldBook

20. Manage Trials
You can view existing locations or create new locations for trials

21. View the Data

22. Funding and Acknowledgements