1. Jing Yu 1, Sook Jung 1, Chun-Huai Cheng 1, Stephen Ficklin 1, Taein Lee 1, Ping Zheng 1, Don Jones 2, Richard Percy 3, Dorrie Main 1 1. Washington State University, 2. Cotton Incorporated, 3. USDA-ARS

2.  A community database to further enable basic, translational and applied cotton research.  Built using the open-source, user-friendly, Tripal database infrastructure used by several other databases  Replaced and expands legacy cotton databases to include transcriptome, genome sequence and breeding data, and advanced data mining tools.

3.  Over 270,000 genetic markers consisting of 3,541 RFLPs, 78,340 SSRs, 188,970 SNPs  15,117 germplasm records including 97 populations and 15,020 individual entries  122 traits (108,000 trait and QTL scores)  12,269 digital images of 2,016 germplasm, from USDA- ARS

4.  G. raimondii genome (BGI and JGI), and G. arboreum genome sequences and annotated features (BGI)  245k Genes and Unigenes  Metabolic Pathways (CottonCyc and KEGG) built using the JGI-D5 v2.1 gene models  15,155 references from journal articles, conference proceedings, patents, book chapters, and theses.

5. - Comparison of various maps  CMap - Comparison of various maps Generic Genome Browser  GBrowse - Generic Genome Browser - Java based genome browser. Very fast and scales well to large datasets such as RNASeq and GBS  JBrowse - Java based genome browser. Very fast and scales well to large datasets such as RNASeq and GBS - Metabolic Pathways in Cotton  CottonCyc - Metabolic Pathways in Cotton Basic Local Alignment Search Tool (NCBI and in- house BATCH server)  BLAST - Basic Local Alignment Search Tool (NCBI and in- house BATCH server)

8. How can I find images for ‘A2 103’?

9.  Metabolic pathways for JGI v2.0 G. raimondii (D5) genome assembly  CottonCyc JGI-D5 summary: Pathways:382 Enzymatic Reactions:2044 Transport Reactions:13 Polypeptides:77269 Enzymes:12468 Transporters:262 Compounds:1473

13.  Implement GBrowse-Syn, a GBrowse-based synteny browser.  Enable community curation of predicted genes using GenSAS  Develop the Cotton Breeders ToolBox.  Add germplasm evaluation data from ARS College Station  Add US National Variety Trials data and make fully searchable  Become current with QTL and QTL mapping data

14.  Industry Funding Cotton Incorporated, Bayer CropScience, Dow/Phytogen, Monsanto, Association of Agricultural Experiment Station Directors  Government Funding USDA ARS USDA NIFA NRSP 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