Differential gene expression in tall fescue tissues in response to water deficit

Authors: CHAKRABARTI, MANOHAR - University Of Kentucky; NAGABHYRU, PADMAJA - University Of Kentucky; SCHARDL, CHRISTOPHER - University Of Kentucky; Dinkins, Randy

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/3/2022
Publication Date: 3/23/2022
Citation: Chakrabarti, M., Nagabhyru, P., Schardl, C.L., Dinkins, R.D. 2022. Differential gene expression in tall fescue tissues in response to water deficit. The Plant Genome. 15:e20199. https://doi.org/10.1002/tpg2.20199.
DOI: https://doi.org/10.1002/tpg2.20199

Interpretive Summary: Tall fescue (Lolium arundinaceum) is a popular pasture and turf grass in much of the U.S., and is particularly known for drought resistance that contributes to its persistence in locations that are unfavorable for other cool-season grasses. Also, its seed-borne fungal symbiont (endophyte) Epichloë coenophiala, which resides in the vegetative plant mainly in the crown (Cr) and pseudostem (Ps), can be a contributing factor in its drought tolerance. Because it contains the apical meristems, Cr survival under drought stress is critical to plant survival. In this study we subjected tall fescue plants with their endophytes to water-deficit stress or, as controls, normal watering, then compared plant transcriptome responses in four vegetative tissues: leaf blades (Lf), Ps, Cr and roots (Rt). A transcript was designated a differentially expressed gene (DEG) if it exhibited at least a 2-fold expression difference between stress and control samples with an adjusted P-value of 0.001. Pathway analysis of the DEGs across all tissue types included photosynthesis, carbohydrate metabolism, phytohormone biosynthesis and signaling, cellular organization, and a transcriptional regulation. Although no set of DEGs was specific to Cr, genes encoding auxin response factors, nuclear pore anchor, structural maintenance of chromosomes and class XI myosin proteins were more highly expressed in Cr than in the other vegetative tissues, suggesting that induction of these genes under stress may aid in survival of the apical meristems.

Technical Abstract: Tall fescue is grown as a pasture, forage, turf and amenity grass throughout the contiguous United States, especially from Missouri and Arkansas to the Eastern Seaboard, and from near the Great Lakes almost to the Gulf Coast. The plant is especially known for greater tolerance to drought stress than is typical for other cool-season grasses, and because it remains active and productive even after episodes of drought, it has an important niche as forage for livestock. A contributing factor in tall fescue productivity and persistence has been shown to be through the beneficial symbiosis with the endophytic fungus, Epichloë coenophiala. Tall fescue has a bunch-type growth habit with tillers emerging from the crown. In its vegetative state each tiller is composed of a lower whorl of leaf sheathes called a pseudostem, topped by the leaf blade. The crown is located near the soil surface and houses the growing points (“meristems”) for tillers and roots, so it is most important for survival of the plant and the crown’s tolerance of stresses is especially critical. Similarly, the endophyte also relies on the survival of the crown during death of the above ground vegetation during the summer droughts, and winter, as it does not reproduce sexually, but continued survival is through the plant seeds. In order to gain insight into mechanisms for tall fescue drought tolerance, changes in gene expression were investigated at the genomic (transcriptome) level in leaf blades, pseudostems, crowns and roots of plants that were either well-watered or subjected to a brief but severe drought. The test plants possessed their native endophytes in order to represent their natural condition. Gene expression was monitored using RNA-seq technology, and the genes that were expressed differently under the stress treatment compared to the normal watering treatment were analyzed. Genes involved in photosynthesis, carbohydrate metabolism, hormone biosynthesis and signaling and gene regulation were significantly affected in response to the imposed stress in all tissues. While no specific genetic pathway was observed to be differentially expressed only in the crown, a higher number of genes involved in hormone signaling, namely, the plant hormone auxin, genes encoding proteins involved in nuclear transport and genes encoding proteins that aid in the integrity of the nucleus, were more highly differentially expressed in the crown than other tissues. While it is still unknown how, or if, the endophyte contributes to these observed gene expression changes, it suggests that expression of these genes may aid in the survival of the crown, and the fungal endophyte in the crown, under stress conditions.