Transcript 2016-01 Plant and Animal Genome XXIV Conference

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
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Introduction
• About CottonGen
• Available data and tools
• How to access CottonGen
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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
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Work in Progress and Future Plans
• 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
Genomics
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Annotated genome sequences (A2, D5, and AD1)
Annotated Gossypium unigenes (v1.0)
CottonCyc metabolic pathways
Genetics and Breeding
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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
Align sequences against all
sequence datasets using
NCBI and Batch BLAST
View and compare 49 genetic
maps using CMap with links into
marker and QTL details pages
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
http://www.cottongen.org
Search Dropdown
Query Examples
 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
 To get all germplasm images, simply click ‘Submit’
 Fill in words that contained in ‘Name’ or ‘Legend’ to
narrow down search result
Further exploration on germplasm ‘7263 NLLY’
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Add G. barbadense genome data
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Add more Map, QTL and trait data
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Further development of a Breeding Information
Management System (BIMS)
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Add more of USDA-ARS germplasm images
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Add Cotton Variety Test data and make them searchable
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