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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #307380

Research Project: Developing Genomic and Genetic Tools for Exploiting Cotton Genetic Variation

Location: Crop Germplasm Research

Title: CottonGen: a genomics, genetics and breeding database for cotton research

item Yu, Jing
item Jung, Sook
item Cheng, Chun-huai
item Ficklin, Stephen
item Lee, Taein
item Zheng, Ping
item Jones, Don
item Percy, Richard
item Main, Dorrie

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2013
Publication Date: 11/6/2013
Citation: Yu, J., Jung, S., Cheng, C., Ficklin, S.P., Lee, T., Zheng, P., Jones, D., Percy, R.G., Main, D. 2013. CottonGen: A genomics, genetics and breeding database for cotton research. Nucleic Acids Research. 42(Database):D1229-D1236.

Interpretive Summary: Free and open access to scientific knowledge and data is essential to healthy public sector research. Prior to 2012, three online databases, CottonDB, CMD and TropGene traditionally hosted much of the available genomic and genetic cotton data. However, individually these three databases had limitations of content, difficulty of access due to older technology, and limited capabilities for integration of differing data types. CottonGen was created to address these limitations by consolidating and expanding cotton data from CottonDB, CMD and TropGene into a new, standards-based, freely accessible scientific database for worldwide cotton research. A feature developed in CottonDB but adopted by CottonGen is the hosting of the website for the International Cotton Genome Initiative (ICGI), thereby tying international research communication and coordination to the data generated by their efforts. CottonGen is now the consolidated cotton genomics, genetics and breeding database for the cotton community. It aims to provide a comprehensive, integrated, online resource that serves basic, translational and applied cotton research.

Technical Abstract: CottonGen ( is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, 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.