Transcriptome profiling of Lolium and Festuca spp leaf and root under drought conditions

Ryegrasses (Lolium spp.) and fescue (Festuca spp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their trait biology. We have compared patterns of differential gene expression in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of Italian ryegrass (festulolium) and meadow fescue with the onset of water stress, focussing on overall patterns of differential gene expression and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation), 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated between 35/15, 35/5, 35/1, 15/5 and 5/1 EWCs from RNAseq data using a combination of DESeq2, edgeR and limma-voom methods.For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. Individual GOs (with the exception of those involved in photosynthesis) were also often enriched by both up- and down-regulated DEGs in the leaf tissue, whereas in the root, generally, only by either up- or down-regulated DEGs. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5-15% of the DEGs enriching the same GO terms were in common to all 4 genotypes, suggesting considerable gene expression variation between related genotypes in enacting the same biological processes.