Transcriptome Analysis and Differential Expression in Tall Fescue Harboring Different Endophyte Strains in Response to Water Deficit

Abstract

Core Ideas RNA‐seq was performed on four tall fescue clone pairs. Three Epichloë coenophiala strains were evaluated. Gene expression was compared for stressed and unstressed plants. Differentially expressed unigenes were identified. Few positive endophyte effects on stress tolerance were observed. Two tall fescue [Lolium arundinaceum (Schreb.) Darbysh. = Schedonorus arundinaceus (Schreb.) Dumort. = Festuca arundinacea var. arundinacea Schreb.] plant genotypes with an Epichloë coenophiala (Morgan‐Jones & W. Gams) C.W. Bacon & Schardl common toxic endophyte (CTE), one with a nontoxic strain (NTE19) and one with another Epichloë species (FaTG‐4) were evaluated and compared with their respective endophyte‐free clones for responses to water‐deficit stress in the greenhouse. One of the plant genotypes (P27) showed a positive effect of its CTE strain on tiller production after stress and resumed watering. In transcriptome analysis of the pseudostems (leaf sheath whorls), differentially expressed genes (DEGs) were defined as having at least twofold expression difference and false discovery rate (FDR) < 0.05 in comparisons of water treatment (stressed or watered), endophyte presence or absence, or both. Stress affected 38% of the plant transcripts including those for the expected stress‐response pathways. The DEGs affected by endophyte in stressed plants were unique to individual plant genotypes. In unstressed plants, endophyte presence tended to reduce expression of genes putatively for defense against fungi, but in unstressed P27 endophyte presence there was enhanced expression of dehydrin and heat shock protein genes. Our results indicated subtle and variable effects of endophytes on tall fescue gene expression; where the endophyte confers protection, its effects on plant gene expression may help prime the plant for stress resistance.

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

“…Table 5 summarizes the latest achievements in this field, including the host plant, endophytic strain, and type of interaction. Induction of stress pathways in response to water deficit [150] It has been evidenced that both endophytic bacterial representatives (Bacillus, Arthrobacter, Nocardiopsis) and fungal endophytes (Gilmaniella, Colletotrichum, Serendipita, Trichoderma) support the defense mechanisms in plants and, consequently, their presence is extremely desirable from the agricultural point of view (Table 5).…”

“…The activation of host (Cacao) genes involved in defense against biotic stresses was demonstrated in the presence of endophytic fungi Colletotrichum and Serendipita [147][148][149]. Moreover, it has been suggested that Trichoderma representatives display distinctly different transcriptional maize root recognition and active colonization, which is connected with the regulation of genes encoding phytohormones and cell wall degradation [150].…”

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes

“…However, the results reported here do indicate that genetic variation between the three genotypes has significant and measurable impacts on patterns of gene expression in response to water stress. The fact that such variation should exist is not surprising and there are numerous examples of gene-expression studies and QTL analyses for different aspects of drought tolerance in forage and other grasses (e.g., Alm et al, 2011 ; Merewitz et al, 2014 ; Baldoni et al, 2016 ; Jiang et al, 2017 ; Liang et al, 2017 ; Zhu et al, 2017 ; Cheruiyot et al, 2018 ; Hu et al, 2018 ; Ji et al, 2018 ; Kumar et al, 2018 ; Ling et al, 2018 ; Ma et al, 2018 ; Chaichi et al, 2019 ; Dinkins et al, 2019 ; Fradera-Sola et al, 2019 ). However, in the context of Brachiaria breeding, these genotypes were selected from a cultivar development program and the results suggest selectable variation with measurable impacts.…”

“…While many studies on differential gene expression in response to water stress have been published on grass species, particularly the major cereals, there is only a limited body of knowledge on water stress-related changes in patterns of gene expression in forage grasses ( Foito et al, 2009 ; Liu and Jiang, 2010 ; Pan et al, 2016 ; Zhao et al, 2016 ; Zhu et al, 2017 ; Ji et al, 2018 ; Dinkins et al, 2019 ; Fradera-Sola et al, 2019 ), the majority of which focus on temperate C 3 forages. Drought tolerance of breeding selections is routinely evaluated in the CIAT forage breeding program, including measuring water extraction under progressive drying soil conditions – for which variation exists across apomictic Brachiaria germplasm.…”

Examining the Impacts of CO2 Concentration and Genetic Compatibility on Perennial Ryegrass—Epichloë festucae var lolii Interactions

“…A more targeted metabolomics approach, using internal standards, would also be warranted to explore in more depth some of the changes we observed in the present experiment. A useful extension of our proteomics analysis would be to examine in more depth some of the protein abundance changes we observed, perhaps coupled with a targeted transcriptomic assay [ 97 ]. Finally, although we recognize that this would be a major undertaking, work should be done to identify the entire plant microbiome, how it changes with different epichloid strains, and its functional role in altering the plant growth, metabolomic, and proteomic responses to climatic change.…”