Additional file 1 of Accurate determination of genotypic variance of cell wall characteristics of a Populus trichocarpa pedigree using high-throughput pyrolysis-molecular beam mass spectrometry
Creators: name: Harman-Ware, Anne E.
name: Macaya-Sanz, David
name: Chanaka Roshan Abeyratne
name: Crissa Doeppke
name: Haiby, Kathleen
name: Tuskan, Gerald A.
name: Stanton, Brian
name: DiFazio, Stephen P.
name: Davis, Mark F.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Ecology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology

description: Additional file 1: Table S1. Quality control metrics for validation and comparison of sample analysis before and after cleaning on the basis of Aspen controls. Parentheses indicate standard deviation. Table S2. Summary of quality control composition metrics determined for P. trichocarpa pedigree samples. Parentheses indicate standard deviation. Values are determined prior to TPS and tray correction. *Two samples were analyzed once. Table S3. Annotations of ions in py-MBMS spectra (supplied as separate file). Table S4. Summary of variance, maternal and paternal effects of each ion after TPS and tray correction (supplied as separate file). Table S5. Comprehensive list of ions in 8 clusters from HC-SRC (supplied as separate file). Table S6. Additional identifier information associated with parents of the P. trichocarpa population. Table S7. Estimates of broad sense heritability for studies in the Salicaceae that used py-MBMS to estimate total lignin and/or S/G ratios for species from the Salicaceae. Figure S1. PCA of standards analyzed throughout course of poplar analysis. Scores plots with numbers at each point indicate the tray (chronological sequence) number associated with particular sample. A) Entire scores plot of all standards, B) zoomed scores plot of region consisting primarily of Center for Bioenergy Innovation (CBI) poplar, Aspen and Poplar 068, C) scores of Loblolly Pine 6G1 standard, D) scores of NIST 8492 (Populus Deltoides), E) scores of Poplar 93968, F) corresponding loadings of spectra from standards only plotted in spectral format for PC-1 and G) loadings for PC-2 of the standard spectra only. “Pop” corresponds to poplar and “Lob” corresponds to Loblolly pine. Figure S2. Aspen Control analysis throughout course of experiment. A) average spectrum B) variance of each ion. Figure S3. PC-1 as a function of time using Control Aspen spectra (TICnormalized) over the course of analysis by py-MBMS. X-axis values correspond to tray number (chronological sequence) in which the aspen sample was analyzed. &gt;120 trays were analyzed over the course of 6 weeks. Figure S4. PCA analyses of replicate 7x7 poplar sample analyses. Colors show replicates prior to tray and TPS correction. Figure S5. TPS-predicted spectra hierarchical clustering dendrogram where colors show separation of 7 clusters corresponding to K-means clusters (Figure S9). Figure S6. PCA of entire population with spatial location of sample highlighted prior to TPS-tray correction of spectra and after TPS-tray corrections. Figure S7. Broad-sense heritability of ions in py-MBMS spectra with and without tray (A) and TPS (B) correction. Figure S8. Variance of ions in py-MBMS spectra explained from maternal and paternal effects. Figure S9. K-means cluster analysis of ions in spectra from 7x7 pedigree. Figure S10. Hierarchical Clustering (complete linkage, Spearman’s rank correlation distance method) of ions from spectra of entire population after tray and TPS correction. EK# shown corresponding to different colors of ions in dendrogram corresponding with Additional file 4 . Figure S11. Lignin content and composition differences based on maternal and paternal relationships. Figure S12. Clusters of samples after tray and TPS correction (Ward’s Euclidean, 7 clusters). Figure S13. K-means clustering of samples based on spectra after clonal averaging from 7x7 P. trichocarpa pedigree. Figure S14. PCA projection of corrected spectra from population after clonal averaging showing clustering associated with m/z 94 abundance (blue square being lowest, red circle is moderate and green triangle is highest intensity of m/z 94). Figure S15. Comparison of phenolic (m/z 94) and S lignin (m/z 210) derived ions across half-sib families, error shows standard deviation within each family. Figure S16. Block diagram of the progeny field design.