Data from: Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula

Stanton-Geddes J, Paape T, Epstein B, Briskine R, Yoder J, Mudge J, Bharti AK, Farmer AD, Zhou P, Denny R, May GD, Erlandson S, Yakub M, Sugawara M, Sadowsky MJ, Young ND, Tiffin P

Date Published: July 12, 2013

DOI: http://dx.doi.org/10.5061/dryad.pq143

 

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Title StantonGeddes2013_Medicago_plant_data
Downloaded 67 times
Description Spreadsheet of plant phenotype data collected in greenhouse experiment for genome-wide association study. Column headings are: block, pot (individual plant ID), trtmnt (rhizobia treatment applied to the plant, either "rhz_12" for a mixture of two rhizobia strains, or "control" for no rhizobia), HM_accession (Medicago HapMap accession), height_1 (height recorded at about two weeks), leaves_1 (number of leaves at about two weeks), height_2 (intermediate height measurement), height_3 (final height before harvest), branch_3 (number of branches on plant before harvest), flowering date (date first flower observed), nodule_above (number of nodules counted in top 5 cm of roots), nodule_below (number of nodules below 5 cm of root growth). More information is available in the R markdown script "StantonGeddes2013_script.Rmd" that accompanies this file.
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Title R script for accession phenotypes
Downloaded 48 times
Description R markdown script used to generate the accession means that were used in the genome-wide association analysis using the TASSEL program.
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Title StantonGeddes2013_Medicago_leaf_data
Downloaded 42 times
Description Spreadsheet of plant leaf data collected by Mohammed Yakub for genome-wide association analysis. Columns are: pot (unique ID that corresponds to plants in "StantonGeddes2013_Medicago_plant_data.csv" file), Trichomes (number of trichomes in the 2 mm long area immediately below the leaf), width mm (width of the petiole in the area where trichomes were counted), petiole area (petiole width times 2 cm), leaf area (area estimated from leaf scan by ImageJ), leaf weight (weight of each leaf after at least 24 hours of drying)
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Title StantonGeddes2013_Medicago_nodule_occupancy
Downloaded 61 times
Description Spreadsheet of nodule occupancy data, described in more detail in README file.
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Title R script for nodule occupancy accession phenotypes
Downloaded 43 times
Description R script to calculate rhizobia strain nodule occupancy for genome-wide association analysis.
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Title README for Tassel analysis
Downloaded 207 times
Description PDF file that describes how Tassel analysis was performed, and analysis of resulting data with R scripts
Download MtHap_GWA_README.pdf (109.2 Kb)
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Title shell script for Tassel analysis
Downloaded 40 times
Description Portable Bash System (PBS) shell script for Tassel analysis run on Minnesota Supercomputing Institute servers
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Title R script for Tassel analysis
Downloaded 66 times
Description R script called by PBS shell script to analyse results of Tassel
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Title R functions for Tassel analysis
Downloaded 74 times
Description Functions required by R for analysis of Tassel results
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When using this data, please cite the original publication:

Stanton-Geddes J, Paape T, Epstein B, Briskine R, Yoder J, Mudge J, Bharti AK, Farmer AD, Zhou P, Denny R, May GD, Erlandson S, Yakub M, Sugawara M, Sadowsky MJ, Young ND, Tiffin P (2013) Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula. PLoS ONE 8(5): e65688. http://dx.doi.org/10.1371/journal.pone.0065688

Additionally, please cite the Dryad data package:

Stanton-Geddes J, Paape T, Epstein B, Briskine R, Yoder J, Mudge J, Bharti AK, Farmer AD, Zhou P, Denny R, May GD, Erlandson S, Yakub M, Sugawara M, Sadowsky MJ, Young ND, Tiffin P (2013) Data from: Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.pq143
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