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

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• CottonGen has served as an integrated genomics platform for cotton research since 2012.
• It consolidated resources from CottonDB and Cotton Marker Database, developing advanced analytical capabilities.
• The platform has undergone substantial expansion between 2021 and 2025.

Purpose of the Study:

• To detail the recent enhancements and expanded capabilities of the CottonGen platform.
• To highlight how CottonGen supports diverse cotton research applications.
• To underscore its role as a central resource for the global cotton research community.

Main Methods:

• Integration of updated Tripal modules for genome-wide association studies (GWAS) and gene expression analysis.
• Implementation of Genotype Investigator for interactive, large-scale genotyping data exploration.
• Enhancement of search and visualization tools, including Map Viewer and Breeding Information Management System.

Main Results:

• A 3-fold increase in tetraploid genome assemblies and gene annotations.
• Doubling of genotype datasets and a 1.8-fold growth in phenotype records.
• Expanded integrated analysis workflows for sequence similarity, synteny, expression profiling, marker-trait association, and breeding data management.

Conclusions:

• CottonGen provides a comprehensive and evolving resource for cotton genomics.
• The platform's enhanced analytical tools facilitate diverse research from gene discovery to marker-assisted selection.
• It plays a crucial role in coordinating global cotton research efforts and supporting cultivar development.