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ARS Home » Southeast Area » Florence, South Carolina » Coastal Plain Soil, Water and Plant Conservation Research » Research » Publications at this Location » Publication #429402
Research Project: Advancing Cotton Genetics and Innovative Cropping Systems for Improved Quality and Production

Location: Coastal Plain Soil, Water and Plant Conservation Research

Title: CottonGen 2025: a knowledgebase for cotton genomics, genetics, and breeding research

Author
item YU, JING - Washington State University
item JUNG, SOOK - Washington State University
item CHENG, CHUN-HUAI - Washington State University
item LEE, TAEIN - Washington State University
item ZHENG, PING - Washington State University
item BUBLE, KATHERYN - Washington State University
item HUMANN, JODI - Washington State University
item JONES, DON - Cotton, Inc
item Campbell, Benjamin
item Udall, Joshua

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2025
Publication Date: 1/20/2026
Citation: Yu, J., Jung, S., Cheng, C., Lee, T., Zheng, P., Buble, K., Humann, J., Jones, D.C., Campbell, B.T., Udall, J.A. 2026. CottonGen 2025: a knowledgebase for cotton genomics, genetics, and breeding research. Genetics. 232(4). https://doi.org/10.1093/genetics/iyaf243.
DOI: https://doi.org/10.1093/genetics/iyaf243

Interpretive Summary: CottonGen (https://www.cottongen.org) serves as an integrated genomics platform for the cotton research community, combining comprehensive data storage with sophisticated analysis tools built on the Tripal framework. Since its establishment in 2012, CottonGen has consolidated and expanded resources previously scattered across CottonDB and the Cotton Marker Database while developing advanced analytical capabilities. The platform has expanded substantially between 2021 and 2025, with tetraploid genome assemblies and gene annotations increasing threefold, genotype datasets doubling, and phenotype records growing 1.8-fold. Recent developments include enhanced search and visualization capabilities, integration of genome-wide association studies and gene expression analysis, and implementation of interactive large-scale genotyping data exploration. Beyond data storage, CottonGen provides integrated analysis workflows spanning sequence similarity searches, synteny analysis, expression profiling, marker-trait association studies, and breeding data management. These capabilities support diverse research applications from comparative genomics and gene discovery to marker-assisted selection and cultivar development. As the official platform for the International Cotton Genome Initiative, CottonGen helps coordinate global cotton research efforts and maintains a comprehensive, actively curated resource that evolves with community research priorities.

Technical Abstract: CottonGen (https://www.cottongen.org) serves as an integrated genomics platform for the cotton research community, combining comprehensive data storage with sophisticated analysis tools built on the Tripal framework. Since its establishment in 2012, CottonGen has consolidated and expanded resources previously scattered across CottonDB and the Cotton Marker Database while developing advanced analytical capabilities. The platform has expanded substantially between 2021 and 2025, with tetraploid genome assemblies and gene annotations increasing threefold, genotype datasets doubling, and phenotype records growing 1.8-fold. Recent developments include enhanced search and visualization capabilities through updated Map Viewer and BIMS tools, integration of genome-wide association studies (GWAS) and gene expression analysis via new Tripal modules, and implementation of GIGWA for interactive large-scale genotyping data exploration. Beyond data storage, CottonGen provides integrated analysis workflows spanning sequence similarity searches, synteny analysis, expression profiling, marker-trait association studies, and breeding data management. These capabilities support diverse research applications from comparative genomics and gene discovery to marker-assisted selection and cultivar development. As the official platform for the International Cotton Genome Initiative (ICGI), CottonGen helps coordinate global cotton research efforts and maintains a comprehensive, actively curated resource that evolves with community research priorities.