1. 2016 Beltwide Cotton Conference
Updates to CottonGen
The Community Database for Genomics, Genetics and Breeding Research in Cotton
Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Katheryn Buble, Ping Zheng, Jodi L. Humann, Deah McGaughey, Heidi Hough, Stephen P. Ficklin, B. Todd Campbell, Richard G. Percy, Don C. Jones, Dorrie Main
2016 Beltwide Cotton Conference
January, 2016
New Orleans, Louisiana

2. Outline Introduction About CottonGen Available data and tools
How to access CottonGen
Query examples
Find germplasm images
Find all germplasm with okra leave shape
Work in Progress and Future Plans

3. About CottonGen
CottonGen is an online genomics, genetics and breeding (GGB) database, designed to help facilitate basic, translational and applied research in cotton
Initiated in 2012 it consolidates and expands CottonDB and the Cotton Marker Database using an open source, modular, resource efficient, actively developed software called Trial
It integrates curated publicly available GGB data into a single portal with a suite of querying and analysis tools
Hosts the ICGI website within it and serves as a communication portal for cotton GGB science

4. Data Summary Genomics Genetics and Breeding
Annotated genome sequences (A2, D5, and AD1)
Annotated Gossypium unigenes (v1.0)
CottonCyc metabolic pathways
Genetics and Breeding
276K genetic markers
49 genetic maps
1000 QTL loci for 200 QTLs
16K germplasm from 6 collections
492K trait scores from germplasm evaluations of US NCGC, GRIN, China and Uzbekistan.
12K digital images of 2K germplasm from USDA-ARS NCGC
610K sequences consisting mostly of  GenBank
15K references   

5. Available Tools
View and compare 49 genetic maps using CMap with links into marker and QTL details pages
Align sequences against all sequence datasets using NCBI and Batch BLAST

6. Available Tools Also GetSeq to retrieve any sequence data in CottonGen
Browse and search the Cotton Genes Metabolic Pathways Database
View and search genome sequence, genes, mapped markers, etc. using GBrowse and JBrowse
Also GetSeq to retrieve any sequence data in CottonGen

7. How to Access CottonGen

8. Redesigned CottonGen Website

9. Redesigned CottonGen Website

10. Species Dropdown: Links to Species Data and Tools

11. Data Dropdown

12. Data Dropdown -> Trait
Search Dropdown

13. Query Examples

14. Find germplasm images Step1: Data Dropdown → Germplasm
Step2: Germplasm page → Browse or search by Image

15. Find germplasm images
To get all germplasm images, simply click ‘Submit’

16. Find germplasm images
Fill in words that contained in ‘Name’ or ‘Legend’ can help to narrow down your search result

17. Find all germplasm with okra leave shape
Step1: Search Dropdown → Trait
Step2: Search Trait → Search Qualitative Traits

18. Find all germplasm with okra leave shape
Step3: Trait Evaluation Search → select trait=leaf shape (NCGC) & value=okra → Submit

19. Find all germplasm with okra leave shape
Further exploration on germplasm ‘7263 NLLY’

20. Further exploration on germplasm ‘7263 NLLY’

21. Future Work Add G. barbadense genome data Add more QTL and trait data
Further development of a Breeding Information Management System (BIMS)
Add more of USDA-ARS germplasm images
Add Cotton Variety Test data and make them searchable

22. Acknowledgements Industry Funding Government Funding
Cotton Incorporated, Bayer CropScience, Dow/Phytogen, Monsanto, Association of Agricultural Experiment Station Directors
Government Funding
USDA NIFA NRSP 10, USDA-ARS and SCRI programs (funding Mainlab Tripal and GenSAS Development)
University Support
Washington State University, Texas A&M, Clemson University
Community of Cotton Researchers and Bioinformatics Researchers

23. Thank You & Question?