3.5 Expression of one-third of drought-responsive genes was not affected by Fld presence
Clustering of DE transcripts allows identification of gene groups that display similar expression patterns and presumably share common regulatory pathways. Total leaf transcripts detected in our microarray were thus grouped into 47 clusters of widely different size. The most highly populated one (27622 members, corresponding to ~85% of all leaf-expressed genes) included those transcripts whose levels were not affected by treatment or genotype. Of the remaining 46 clusters containing genes differentially expressed in response to water limitation and/or Fld presence (4847 DE genes), we focused in 17 clusters that were either highly populated or enriched in pathways and functional categories associated to stress responses, redox biochemistry and chloroplast functions, comparing vis-à-vis those that exhibit contrasting expression behaviors (e.g ., induction vs. repression). Distribution of DE transcripts in these 17 clusters can be found in Supplementary Tables S4-9, and the responses represented by the other 29 clusters are described in Supplementary Figure S4.
Clusters comprising genes that display a similar drought response in the presence or absence of Fld represent 31.5% of total DE transcripts, of which 601 were induced (cluster 1) and 929 were repressed (cluster 2). Cluster 1 was enriched in genes coding for components of the cytosolic branch of glycolysis, ethylene synthesis, heat stress and signal transduction associated to abscisic acid (Supplementary Figure S5; Supplementary Table S4). Cluster 2 exhibited a remarkable over-representation of genes belonging to cell wall metabolism such as cellulose synthases, cellulases and pectinesterases, which declined in both lines under water deficit (Supplementary Figure S5; Supplementary Table S4). Several receptor kinases of the leucine-rich repeat family were also repressed by drought irrespective of genotype.