Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)

• Published in: PloS one Vol. 14; no. 7; p. e0220518
• Main Authors: Fradera-Sola, Albert, Thomas, Ann, Gasior, Dagmara, Harper, John, Hegarty, Matthew, Armstead, Ian, Fernandez-Fuentes, Narcis
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30.07.2019; Public Library of Science (PLoS)
• Subjects: Acids; Annotations; Biochemistry; Biology; Biology and Life Sciences; Dehydration; Drought; Droughts; Environmental conditions; Environmental quality; Experiments; Flowering; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Ontology; Genes; Genetic aspects; Genetic engineering; Genomes; Genomics; Genotype; Genotype & phenotype; Genotypes; Grasses; Grasslands; Identification; Kinases; Leaves; Lolium - genetics; Lolium - growth & development; Lolium - metabolism; Lolium perenne; Metabolism; Moisture content; Nucleotide sequence; Ontology; Physiology; Plant Leaves - genetics; Plant Leaves - growth & development; Plant Leaves - metabolism; Plant Proteins - genetics; Plant Roots - genetics; Plant Roots - growth & development; Plant Roots - metabolism; Plant tissues; Polyethylene glycol; Rain; Ribonucleic acid; RNA; RNA sequencing; Ryegrasses; Transcriptome; Transformation; Vermiculite; Water; Water availability; Water content; Water quality; Water resources; Water stress; United Kingdom > UK
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0220518

Perennial ryegrass (Lolium perenne) is a forage and amenity grass species widely cultivated in temperate regions worldwide. As such, perennial ryegrass populations are exposed to a range of environmental conditions and stresses on a seasonal basis and from year to year. One source of potential stress is limitation on water availability. The ability of these perennial grasses to be able to withstand and recover after periods of water limitation or drought can be a key component of grassland performance. Thus, we were interested in looking at changes in patterns of gene expression associated with increasing water stress. Clones of a single genotype of perennial ryegrass were grown under non-flowering growth room conditions in vermiculite supplemented with nutrient solution. Leaf and root tissue was sampled at 4 times in quadruplicate relating to estimated water contents of 35%, 15%, 5% and 1%. RNA was extracted and RNAseq used to generate transcriptome profiles at each sampling point. Transcriptomes were assembled using the published reference genome sequence and differential gene expression analysed using 3 different programmes, DESeq2, edgeR and limma (with the voom transformation), individually and in combination, deriving Early, Middle and Late stage comparisons. Identified differentially expressed genes were then associated with enriched GO terms using BLAST2GO. For the leaf, up-regulated differentially expressed genes were strongly associated with GO terms only during the Early stage and the majority of GO terms were associated with only down-regulated genes at the Middle or Late stages. For the roots, few differentially expressed genes were identified at either Early or Middle stages. Only one replicate at 1% estimated water content produced high quality data for the root, however, this indicated a high level of differential expression. Again the majority of enriched GO terms were associated with down-regulated genes. The performance of the different analysis programmes and the annotations associated with identified differentially expressed genes is discussed.