Updates to the CSFL Genome Database: Resources for pea, lentil, faba bean and chickpea genetics, genomics and breeding www.coolseasonfoodlegume.org 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

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

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

CSFL Homepage

Crop Overview Pages

Data Searches

Data Searches

Available Tools

BLAST

BLAST

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

PathwayCyc Pathway Tools analysis of C. arietinum CDC Frontier and C. reticulatum PI 489777 genomes C. arietinum ICC 4958 in progress and will be available soon

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.

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

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.

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

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

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

Data Import from Templates or FieldBook

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

View the Data

Funding and Acknowledgements