Datasets to build marker effect networks
2023-01-23
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Datasets to build marker effect networks
Published Date
2023-01-23
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Hirsch, Candice N
cnhirsch@umn.edu
cnhirsch@umn.edu
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Experimental Data
Field Study Data
Genomics Data
Experimental Data
Field Study Data
Genomics Data
Abstract
This dataset contains the input files to build marker effect networks and identify markers associated with environmental adaptability. These networks are built by adapting commonly used software for building gene co-expression networks with marker effects across growth environments as the input data into the networks. Here, we provide grain yield data from 400 maize hybrids grown across nine environments in the U.S. Midwest, a set of ~10,000 non-redundant markers, and environmental data containing 17 weather parameters in 3-day intervals collected from planting date to the end of the season. For instructions on how to perform this analysis and analysis script, please see https://github.com/HirschLabUMN/meffs_networks. For more details on marker effect networks, please see preprint on https://www.biorxiv.org/content/10.1101/2023.01.19.524532v1.
Description
Files include yield data (raw and BLUEs) of maize hybrids across different growth environments, genotypic data of maize inbred lines (parental and RILs) and hybrids, and environmental covariates data. More detailed information for each file can be found in the README file.
Referenced by
Rafael Della Coletta, Sharon E. Liese, Samuel B. Fernandes, Mark A. Mikel, Martin O. Bohn, Alexander E. Lipka, Candice N. Hirsch. 2023. Linking genetic and environmental factors through marker effect networks to understand trait plasticity. bioRxiv.
https://doi.org/10.1101/2023.01.19.524532
https://doi.org/10.1101/2023.01.19.524532
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United States Department of Agriculture (2018-67013-27571)
Minnesota Agricultural Experiment Station
Minnesota Agricultural Experiment Station
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Suggested citation
Della Coletta, Rafael; Liese, Sharon E; Fernandes, Samuel B; Mikel, Mark A; Bohn, Martin O; Lipka, Alexander E; Hirsch, Candice N. (2023). Datasets to build marker effect networks. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/b1e0-q828.
View/Download file
| File View/Open | Description | Size |
|---|---|---|
| supp_file1.csv | Raw yield data of maize hybrids across different growth environments | 1.15 MB |
| supp_file2.txt | Best Linear Unbiased Estimates (BLUEs) of maize hybrids within each environment | 92.72 KB |
| supp_file3.hmp.txt | Raw genotypic data of maize parental lines in hapmap format | 1.41 MB |
| supp_file4.hmp.txt | Raw genotypic data of recombinant inbred lines (RILs) in hapmap format | 20.2 MB |
| supp_file5.hmp.txt | Filtered genotypic data of maize hybrids derived from RILs in hapmap format | 12.31 MB |
| supp_file6.txt | Environmental covariates data | 253.93 KB |
| README.txt | Description of the data | 11.85 KB |
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