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

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

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

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   

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

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

How to Access CottonGen

Redesigned CottonGen Website http://www.cottongen.org

Redesigned CottonGen Website

Species Dropdown: Links to Species Data and Tools

Data Dropdown

Data Dropdown -> Trait Search Dropdown

Query Examples

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

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

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

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

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

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

Further exploration on germplasm ‘7263 NLLY’

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

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

Thank You & Question?