Skip to main content
ARS Home » Southeast Area » Florence, South Carolina » Coastal Plain Soil, Water and Plant Conservation Research » Research » Publications at this Location » Publication #387730
Research Project: Effective Cotton Genetics and Management Practices for Improved Cotton Quality and Production

Location: Coastal Plain Soil, Water and Plant Conservation Research

Title: CottonGen: the community database 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, TAIN - Washington State University
item ZHENG, PING - Washington State University
item BUBLE, KATHERYN - Washington State University
item CRABB, JAMES - Washington State University
item HUMANN, JODI - Washington State University
item HOUGH, HEIDI - Washington State University
item JONES, DON - Cotton, Inc
item Campbell, Benjamin - Todd
item Udall, Joshua - Josh
item MAIN, DORRIE - Washington State University

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2021
Publication Date: 12/18/2021
Citation: Yu, J., Jung, S., Cheng, C., Lee, T., Zheng, P., Buble, K., Crabb, J., Humann, J., Hough, H., Jones, D., Campbell, B.T., Udall, J.A., Main, D. 2021. CottonGen: the community database for cotton genomics, genetics, and breeding research . Plants. 10(12):2805. https://doi.org/10.3390/plants10122805.
DOI: https://doi.org/10.3390/plants10122805

Interpretive Summary: Today, breeding programs are producing ever larger amounts of big data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System, a free, secure, and online breeding management system that allows breeders to store, manage, archive, and analyze their private breeding data. Breeding Information Management System is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. Breeding Information Management System incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. Breeding Information Management System comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium.

Technical Abstract: In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System, a free, secure, and online breeding management system that allows breeders to store, manage, archive, and analyze their private breeding data. Breeding Information Management System is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. Breeding Information Management System incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. Breeding Information Management System comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium.