1. Updates to CottonGen: The Community Database for Genomics, Genetics and Breeding Research in Cotton
Plant and Animal Genome Conference XXIV
Jing Yu1, Sook Jung1, Chun-Huai Cheng1, Taein Lee1, Katheryn Buble1, Ping Zheng1, Jodi L. Humann1, Deah McGaughey1, Heidi Hough1, Stephen P. Ficklin1, B. Todd Campbell2, Richard G. Percy3, Don C. Jones4 and Dorrie Main1
Washington State University, Pullman, WA, 2. USDA-ARS, Florence, SC, 3. USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, 4.Cotton Incorporated, Cary, NC
corresponding authors:
Abstract
CottonGen ( is the community database for basic, translational and applied research in cotton. Developed using Tripal, an open-source, resource-efficient, standardized platform for biological database construction, it provides an online portal of curated and integrated genomics, genetics and breeding data, combined with a suite of tools facilitating intuitive data mining and analysis. We highlight new data and functionality in CottonGen, with a particular emphasis on application in breeding, and present future plans for development over the next 5 years for this industry, USDA, USDA-ARS funded resource.
Achievements
Data Overview
Annotated A2, D5, and AD1 genome sequences
CottonCyc built using the JGI-D5 v2.1 gene models
276K genetic markers include RFLP, RT-PCR, SSR, SNP
49 maps cover cotton genome groups AD, A, D, and G
1000 QTL loci of 200 QTL trait data from 7 QTL datasets
16K germplasm and 16 collections include US, UZ and China.
492K trait scores from 4 germplasm evaluation projects
12K digital images of 2K germplasm, from USDA-ARS NCGC
@CottonGen_news
data and tools
Further Development Plan
Development of a comprehensive Breeding Information Management System (BIMS)
Further develop data-mining resources for both basic and translational scientists
Add G. barbadense genome and annotation data
Add more curated QTL and trait data
Add the National Cotton Variety Test (NCVT) data
Search Markers
Marker Overview
Maps
QTL Overview
Germplasm Overview Page
CottonCyc
Genome
Germplasm Images
Germplasm Images
Trait Descriptors
Trait Descriptor Standard Images
Acknowledged with Thanks
The Cotton Research Community