Additional file 1 of A high diversity of non-target site resistance mechanisms to acetolactate-synthase (ALS) inhibiting herbicides has evolved within and among field populations of common ragweed (Ambrosia artemisiifolia L.)

Additional file 1: Table S1. Review of previous studies and their experimental design aimed at identifying genetic determinisms of NTSR using a transcriptomic approach. Table S2. Frequencies of plants resistant to imazamox and tribenuron in the six ragweed populations used in this study (source: Loubet et al., 2021). Table S3. Number of individual plants per population and per phenotype in the five batches produced for this study. Table S4. Experimental design of the four RNA sequencing experiments. Table S5. Ranking of all candidate genes for the ability of their expression level to discriminate phenotype obtained by linear discriminant analysis for each of the three populations, ARA2, ARA8 and NAQ8. By default, the top 20 variables are ranked by the caret package. The top 10 were selected for further analysis. Table S6. Genes constitutively DE between resistant and sensitive plant pools (Log2FC and associated adjusted p-value) identified in 4, 3 or 2 populations with plants resistant to tribenuron. Genes with a higher or lower expression in resistant plants compared to sensitive plants are highlighted in orange or in green, respectively. Genes with no DE are highlighted in green. Table S7. Biological processes and molecular functions associated with DE genes significantly enriched in at least 2 populations (elim Fisher test). Table S8. DE genes selected for validation of their potential link with NTSR (genes independently selected in more than one population are highlighted in green). Table S9. Number of genes DE  between resistant and sensitive plant pools in each population before (BT) and/or 2 hours after (2HAT) treatment. Table S10. Genes significantly DE 2HAT between resistant and sensitive plant pools identified in at least 2 populations. Genes with a higher or lower expression in resistant pools compared to sensitive pools are highlighted in orange or in green, respectively. Table S11. Shared biological processes (BPs) or molecular functions (MFs) associated to genes DE between resistant and sensitive plants 2HAT in at least 2 populations (elim Fisher test). Table S12. Number of genes DE  before and after treatment for each phenotype and each population. Supplementary Table S13. Complementary statistics obtained in the establishment of phenotype prediction models by LDA with LOOCV resampling. Table S14. relative expression level of candidate genes  measured by qPCR in populations ARA2, ARA8 and NAQ8 on plants in batches used for RNASeq (batches 1, 2 and 3a) and on an additional, independent batch (batch 4) (see Table S3). Table S15. Summary of the genes family associated with NTSR to herbicides in weeds identified in RNA sequencing studies ; genes identified in our study are highlighted in orange.