Supplementary Data of the paper: An in-situ characterization of Triticum aestivum sheds light on the role of wheat genotype and agricultural practices on the below-ground microbiota

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Here we provided supplementary datasets of the article: An in-situ characterization of Triticum aestivum sheds light on the role of wheat genotype and agricultural practices on the below-ground microbiota. In particular raw data and supplementary figures are reported here as well supplementary tables obtained from statistical analysis. In the excel file are reported: Table S1. Genotype abbreviated names. Table S2. Primer pairs used for ITS amplification. Red bases indicate the Illumina adaptors, blue bases indicate the internal TAGS used for sample multiplexing, blue bases indicate the ITS2 primer. Table S3. TAGS for demultiplexing the fungal reads in the study SRP587060. r= roots, rh= rhizosphere, fert = fertilized, nfert = control in the fertilization trial, f= faba bean association, nf= control in the faba bean association trial, a=2017, b=2018. Other conditions were not used in this study. Table S3. TAGS for demultiplexing the bacterial reads in the study SRP587039. r= roots, rh= rhizosphere, fert = fertilized, nfert = control in the fertilization trial, f= faba bean association, nf= control in the faba bean association trial, a=2017, b=2018. Other conditions were not used in this study. Table S5. Fungal OTU affiliation. Table S6. Fungal OTU count table. r= roots, rh= rhizosphere, fert = fertilized, nfert = control in the fertilization trial, f= faba bean association, nf= control in the faba bean association trial, a=2017, b=2018. Other conditions were not used in this study. Table S7. Bacterial OTU affiliation. Table S8. Bacterial OTU count table. r= roots, rh= rhizosphere, fert = fertilized, nfert = control in the fertilization trial, f= faba bean association, nf= control in the faba bean association trial, a=2017, b=2018. Other conditions were not used in this study. Table S9. Raw values for both α-diversity and β-diversity indices estimated on the ITS and used for statistical analysis. Table S10. Raw values for both α-diversity and β-diversity indices estimated on the gyrB used for statistical analysis. Table S11. Analysis of deviance table (Type II Wald chisquare tests) for the α-diversity and β-diversity indices in the root and rhizosphere compartments of wheat genotypes grown under different agricultural practices. Bacterial diversity was inferred by using a portion of the gyrB gene and fungal diversity was inferred by using ITS2 marker region. Table S12. Pairwise comparisons for the ITS data set using factor fitting to an ordination for the wheat genotype 2017 dataset (A) and genotype 2018 root compartment dataset (B). P-values have been corrected with FDR method. Table S13. Pairwise comparisons for the gyrB Table using factor fitting to an ordination for the wheat genotype 2017 dataset (A) and genotype 2018 root compartment dataset (B). P-values have been corrected with FDR method. Table S14. BLUPs for the ITS Table. Table S15. BLUPs for the gyrB Table. Table S16. PCoA Axis for plant genotypes. Table S17. sPLSR between axes of the PCoA of the SNPs and microbiota descriptors. Table S18. Linear regressions between axes of the PCoA of the SNPs and microbiota descriptors. Table S19. Wheat phenotypic values. Protein content (protein), Thousand-grain weight (TGW), and Grain yield (yield). In the document file are reported supplementary Figures: Fig S1. Soil texture of the three plots where the wheat assays were conducted in 2016-2017 and 2017-2018. The LH7 plot was used for the 20 wheat genotypes trial and the LH6B plot for the faba bean association trial, in 2016-2017. The LH8 plot was used for the 19 wheat genotypes assays and the fertliziation trial, and the LH6B plot for the faba bean association trial, in 2017-2018. Figure S2. Fungal and bacterial α-diversity estimated for the faba bean association and fertilization trials. Box plots representing the microbiota variation of the α-diversity inferred as Species Richeness for (a) fungal communities estimated by sequencing an ITS fragment and (b) bacterial communities estimated by sequencing a gyrB fragment in roots of wheat from the faba bean association trials (2017-2018) and fertilization trial (2018). y-axes represent the Species Richeness index and x-axes the wheat genotypes. Root and rhizosphere samples are represented. Dark blue represents plants under the treatment (faba bean association or fertilization) and light blue represents the control plants. Figure S3. Box plots representing the wheat genotype microbiota variation of the α-diversity inferred as species richennes for (a) fungal communities estimated by sequencing an ITS fragment and (b) bacterial communities estimated by sequencing a gyrB fragment in wheat roots and rhizospheres collected in 2017 and 2018 on the wheat genotype assay. y-axes represent the species Species Richeness index and x-axes the wheat genotypes. Figure S4. Grid plot for the significant linear regressions found by regressing fungal and bacterial microbiota descriptors (x axis), and wheat genetic distance PCoA axes. R2 and the corresponding P-values corrected for FDR are illustrated for each plot.

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