Supplemental Material for Lin, Lazarus, and Rhee, 2020 Fan Lin Elena Z. Lazarus Seung Rhee 10.25387/g3.11789646.v1 https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Lin_Lazarus_and_Rhee_2020/11789646 <p>Table S1. Known causal genes and their orthologs in major model plants and crop species.</p><p>Table S2. The average value of features used for the Arabidopsis model.</p><p>Table S3. The average value of features used for the rice model.</p><p>Talbe S4. Function annotation, gene expression data, and protein seqeunce difference of thirteen candidate prioritized by QTG-Finder2 and SD1.</p><p>Table S5 putative transcription factor binding sites identified in the promoter of Sevir.5G394900. </p><p><br></p><p>Figure S1 Whole-genome synteny map between Setaria viridis and Setaria italica by SynMap</p><p>Figure S2 Parameter tuning for the Setaria viridis model based on cross-validation AUC-ROC. Error bars represent standard deviation, N=3. <br></p><p>Figure S3 Parameter tuning for the Sorghum bicolor model based on cross-validation AUC-ROC<br></p><p>Figure S4 Causal-gene orthologs in 12 major crops and model species. <br></p><p>Figure S5 Models trained with different groups of orthologs performed similarly according to external validation. <br></p><p>Figure S6 Feature importance of the newly added features to the Arabidopsis and rice models. <br></p><p>Figure S7 Multiple sequence alignment for a RIO2 protein across grass species, yeast and human using Clustal Omega <br></p><p>Figure S8 Multiple sequence alignment for a RIO2 protein across grass species using Clustal Omega <br></p><p>Figure S9 Multiple sequence alignment of a candidate gene SD1 across grass species using Clustal Omega <br></p><p>Figure S10 A candidate gene encoding a ribosomal protein in the L1P family has higher expression in Setaria italica (Seita.5G389700) than in Setaria viridis (Sevir.5G394900). <br></p><p>Figure S11 Pairwise sequence alignment shows polymorphisms in the putative promoters of an ortholog pair of genes encoding L1P ribosomal proteins. <br></p><p><br></p> 2020-05-18 16:50:07 Sorghum bicolor Setaria viridis machine learning quantitative trait loci causal genes Bioinformatics Computational Biology Plant Biology