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CottonGen: Cotton Database Resources

posted on 2024-02-13, 13:43 authored by Jing Yu, Sook Jung, Chun-Huai Cheng, Stephen P. Ficklin, Taein Lee, Ping Zheng, Don Jones, Richard G. Percy, Dorrie Main

CottonGen ( is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data to enable basic, translational and applied research in cotton. Built using the open-source Tripal database infrastructure, CottonGen supersedes CottonDB and the Cotton Marker Database, which includes sequences, genetic and physical maps, genotypic and phenotypic markers and polymorphisms, quantitative trait loci (QTLs), pathogens, germplasm collections and trait evaluations, pedigrees, and relevant bibliographic citations, with enhanced tools for easier data sharing, mining, visualization, and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST.

This project is funded/supported by Cotton Incorporated, the USDA-ARS Crop Germplasm Research Unit at College Station, TX, the Southern Association of Agricultural Experiment Station Directors, Bayer CropScience, Corteva/Agriscience, Dow/Phytogen, Monsanto, Washington State University, and NRSP10.

Resources in this dataset:

  • Resource Title: Website Pointer for CottonGen.

    File Name: Web Page, url:

    Genomic, Genetic and Breeding Resources for Cotton Research Discovery and Crop Improvement organized by :

    • Species (Gossypium arboreum, barbadense, herbaceum, hirsutum, raimondii, others),
    • Data (Contributors, Download, Submission, Community Projects, Archives, Cotton Trait Ontology, Nomenclatures, and links to Variety Testing Data and NCBISRA Datasets),
    • Search options (Colleague, Genes and Transcripts, Genotype, Germplasm, Map, Markers, Publications, QTLs, Sequences, Trait Evaluation, MegaSearch),
    • Tools (BIMS, BLAST+, CottonCyc, JBrowse, Map Viewer, Primer3, Sequence Retrieval, Synteny Viewer),
    • International Cotton Genome Initiative (ICGI), and
    • Help sources (User manual, FAQs).

    Also provides Quick Start links for Major Species and Tools.


Cotton Incorporated

USDA-ARS: Crop Germplasm Research Unit, College Station, TX

Bayer CropScience

Dow Chemical Company: Phytogen

Monsanto Company

Washington State University

USDA-NIFA: 2009-51181-06036

USDA-NIFA: 2009-51181-05808


Data contact name

Main, Dorrie

Data contact email


MainLab, Washington State University

Intended use

To provide access to publicly available genomic, genetic and breeding data to enable basic, translational, and applied research in cotton.

Temporal Extent Start Date



  • Not specified

Geographic Coverage


ISO Topic Category

  • biota
  • boundaries
  • farming

Ag Data Commons Group

  • AgBioData

National Agricultural Library Thesaurus terms

Internet; databases; genomics; breeding; translation (genetics); applied research; cotton; infrastructure; phenotype; quantitative trait loci; pathogens; germplasm conservation; pedigree; unigenes; expressed sequence tags; loci; taxonomy; germplasm; Gossypium raimondii; genetic markers; publications; genetic databases; plant breeding; plant genetics; computer software

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 301

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen P.; Lee, Taein; Zheng, Ping; Jones, Don; Percy, Richard G.; Main, Dorrie (2019). CottonGen: Cotton Database Resources. MainLab, Washington State University.

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