1. 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

2.  Introduction About CottonGen Available data and tools How to access CottonGen  Query examples 1. Find genes by function 2. Find germplasm image 3. Find all germplasm with okra leave shape 4. Find sequences around QTLs for trait  Work in Progress and Future Plans

3. 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. Genomics  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  16K germplasm from 6 sub-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. 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. 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. http://www.cottongen.org

12. Search Dropdown

13. Query Examples

14.  Returns gene matches in a table with description  Browse or download the data  Links to individual gene and all analyses, alignments, homologs, external databases, sequences, etc. CotAD_66845

15.  To get all germplasm images, simply click ‘Submit’  Fill in words that contained in ‘Name’ or ‘Legend’ to narrow down search result

20. Further exploration on germplasm ‘7263 NLLY’

23.  Add G. barbadense genome data  Add more Map, 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

24. Industry 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