Data and code from: The Impacts of Parental Choice and Intrapopulation Selection for Seed Size on the Uprightness of Progeny Derived from Interspecific Hybridization between Glycine max and Glycine soja

<p>This dataset contains all data and code necessary to reproduce the analysis described under the heading "Experiment 3" in the manuscript:</p>
<p>Taliercio, E., Eickholt, D., Read, Q. D., Carter, T., Waldeck, N., & Fallen, B. (2023). Parental choice and seed size impact the uprightness of progeny from interspecific <em>Glycine</em> hybridizations. <em>Crop Science</em>. <a href="https://doi.org/10.1002/csc2.21015">https://doi.org/10.1002/csc2.21015</a></p>
<p>The attached files are:</p>
<ul>
<li>
<p><code>G_max_G_soja_seedweight_seedcolor_analysis.Rmd</code>: RMarkdown notebook containing all analysis code. The CSV data files should be placed in a subdirectory called data within the working directory from which the notebook is rendered.</p>
</li>
<li>
<p><code>G_max_G_soja_seedweight_seedcolor_analysis.html</code>: Rendered HTML output from RMarkdown notebook, including figures, tables, and explanatory text.</p>
</li>
<li>
<p><code>counts_seedwt.csv</code>: CSV file containing the number of progeny selected and average 100-seed weight data for each combination of cross, size class, and replicate. Columns are:</p>
<ul>
<li><strong>F3_location:</strong> text identifier of F3 nursery location, either <code>"CLA"</code> or <code>"FF"</code></li>
<li><strong>plot:</strong> numeric ID of plot</li>
<li><strong>pop:</strong> numeric ID of population</li>
<li><strong>max:</strong> name of G. max parent</li>
<li><strong>soja:</strong> name of G. soja parent</li>
<li><strong>F2_location:</strong> text identifier of F2 nursery location, either <code>"Caswell"</code> or <code>"Hugo"</code></li>
<li><strong>n_planted:</strong> number of seeds planted (raw)</li>
<li><strong>n_selected:</strong> number of progeny selected</li>
<li><strong>size_ordered:</strong> seed size class, to be converted to an ordered factor</li>
<li><strong>size_combined:</strong> seed size class aggregated to fewer unique levels</li>
<li><strong>ave_100sw:</strong> average 100-seed weight for the given size class</li>
<li><strong>n_planted_trials:</strong> number of seeds planted rounded to nearest integer</li>
</ul>
</li>
<li>
<p><code>seedcolor.csv</code>: CSV file with additional data on number of seeds of each color by population. Columns are:</p>
<ul>
<li><strong>cross:</strong> text identifier of cross</li>
<li><strong>line:</strong> text identifier of line</li>
<li><strong>light:</strong> number of light seeds</li>
<li><strong>mid:</strong> number of mid-green seeds</li>
<li><strong>brown:</strong> number of brown seeds</li>
<li><strong>dark:</strong> number of dark or black seeds</li>
<li><strong>population:</strong> identifier of population type (F2 derived or selected)</li>
<li><strong>max:</strong> name of <em>G. max</em> parent</li>
<li><strong>n_total:</strong> sum of the light, mid, brown, and dark columns</li>
<li><strong>soja:</strong> name of <em>G. soja</em> parent</li>
</ul>
</li>
</ul>
<p>The data processing and analysis pipeline in the RMarkdown notebook includes:</p>
<ul>
<li>Importing the data (slightly cleaned version is provided)</li>
<li>Creating boxplots of proportion selected by cross, nursery location, and size class</li>
<li>Fitting logistic GLMM to estimate the probability of selection as a function of parent, 100-seed weight, and their interactions</li>
<li>Extracting and plotting random effect estimates from model</li>
<li>Calculating and plotting estimated marginal means from model</li>
<li>Taking contrasts between pairs of estimated marginal means and trends</li>
<li>Calculating Bayes Factors associated with the contrasts</li>
<li>Generating figures and tables for all above results</li>
<li>Additional seed color analysis: importing data (slightly cleaned version is provided)</li>
<li>Additional seed color analysis: drawing exploratory bar plot</li>
<li>Additional seed color analysis: fitting multinomial GLM modeling the proportion of seeds with each color as a function of population</li>
<li>Additional seed color analysis: generating expected value predictions from GLM and taking contrasts</li>
<li>Additional seed color analysis: creating figures and tables for model results</li>
</ul>
<p>This research was funded by CRIS 6070-21220-069-00D, United Soybean Board Project # 2333-203-0101, and falls under National Program NP301.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: RMarkdown document with all analysis code.</p> <p>File Name: G_max_G_soja_seedweight_seedcolor_analysis.Rmd</p></li><br><li><p>Resource Title: Rendered HTML version of notebook.</p> <p>File Name: G_max_G_soja_seedweight_seedcolor_analysis.html</p></li><br><li><p>Resource Title: Progeny counts and seed weight data.</p> <p>File Name: counts_seedwt.csv</p></li><br><li><p>Resource Title: Seed color counts data.</p> <p>File Name: seedcolor.csv</p></li></ul>

Tags: ars, data-gov, glycine-max, glycine-soja, hybrids, np301, plant-breeding, response-to-selection, seed-size, soybean, uprightness
Organization: Department of Agriculture