Location: Coastal Plain Soil, Water and Plant Conservation Research
Title: CottonGen: the community database for cotton genomics, genetics, and breeding researchAuthor
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YU, JING - Washington State University |
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JUNG, SOOK - Washington State University |
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CHENG, CHUN-HUAI - Washington State University |
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LEE, TAIN - Washington State University |
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ZHENG, PING - Washington State University |
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BUBLE, KATHERYN - Washington State University |
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CRABB, JAMES - Washington State University |
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HUMANN, JODI - Washington State University |
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HOUGH, HEIDI - Washington State University |
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JONES, DON - Cotton, Inc |
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Campbell, Benjamin |
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Udall, Joshua |
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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. |