Extended Data Fig. 3: Differential cotton transcript expression in leaf tissue following foliar application does not reveal stress-related perturbation in response to LDH.

Heatmap of 50 differentially expressed transcripts with lowest p values for a, BioClay vs. water, b, LDH vs. water, and c, naked dsRNA (sucrase) vs Water. BioClay (sucrase dsRNA-LDH) and LDH treatments do not co-cluster in each dataset. d, PCA analysis to differentially expressed transcripts does not demonstrate any clustering or co-clustering of samples from BioClay, LDH, naked dsRNA or water treatments, showing multitranscript treatment-specific impacts are not readily evident. e, Euler diagram of up-regulated transcript counts for BioClay, LDH and naked dsRNA vs. water. Most transcripts are upregulated in all three treatments or in individual treatments. Only 24 transcripts are up-regulated (p < 0.05 and log fold change > 1) in both BioClay and LDH but not naked dsRNA treatments relative to water, with none having identified abiotic stress-related functions (for example, HSps or WRKY, NAC, MYB and AP2/ERF TFs) in this subset. f. Euler diagram of down-regulated transcript counts for BioClay, LDH and naked dsRNA vs. water. Similarly, only 7 transcripts are down-regulated (p < 0.05 and log fold change < −1) in both BioClay and LDH but not naked dsRNA treatments relative to water. These transcripts also did not have identified abiotic stress functions. Total RNA was extracted from leaf tissue 10 days after foliar application (n = 3 for each treatment). Transcript expression analyses including generation of adjusted p-values were performed on generated Illumina paired-end read files using DESeq2 following adapter trimming and QC by Trim Galore and pseudoalignment using Kallisto v.0.46.1. Euler diagrams were plotted using the Eulerr R package v.6.1.1.