Multi-Year Pathogen Survey of Biofuel Switchgrass Breeding Plots Reveals High Prevalence of Infections by Panicum mosaic virus and Its Satellite Virus

Abstract

Switchgrass (Panicum virgatum) cultivars are currently under development as lignocellulosic feedstock. Here we present a survey of three established switchgrass experimental nurseries in Nebraska in which we identified Panicum mosaic virus (PMV) as the most prevalent virus. In 2012, 72% of 139 symptomatic plants tested positive for PMV. Of the PMV-positive samples, 19% were coinfected with its satellite virus (SPMV). Less than 14% of all sampled plants in 2012 were positive for four additional viruses known to infect switchgrass. In 2013, randomized sampling of switchgrass individuals from the same 2012 breeding plots revealed that infection by PMV or PMV+SPMV was both more prevalent and associated with more severe symptoms in the cultivar Summer, and experimental lines with Summer parentage, than populations derived from the cultivar Kanlow. A 3-year analysis, from 2012 to 2014, showed that previously uninfected switchgrass plants acquire PMV or PMV+SPMV between harvest cycles. In contrast, some plants apparently did not maintain PMV infections at detectable levels from year-to-year. These findings suggest that PMV and SPMV should be considered important pathogens of switchgrass and serious potential threats to biofuel crop production efficiency.

Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars

“…Two ecotypes of switchgrass are known, with the lowland ecotypes adapted to wetter regions, and the upland ecotypes adapted to drier conditions. Upland and lowland cultivars of switchgrass differ in their genetics [2–7], yield potential [8–13], upland cultivars are better adapted for cold, winter survival [14–16], and lowland ecotypes exhibit higher resistance to certain pathogens [17–19].…”

Panicum Mosaic Virus and Its Satellites Acquire RNA Modifications Associated with Host-Mediated Antiviral Degradation

“…Paradoxically, PMV is frequently associated with both SPMV and the satellite RNAs (25–28, 30), which have opposing effects on the replication of the helper virus (28, 29, 32). PMV persists for years within an infected host, suggesting a fine-tuned balance between virus replication and host defenses (27). Assuming that many of the modified PMV RNAs are defective for translation, due to loss of enhancer elements in the 3′ UTR and less initiation factor recruitment and RNA sequestration within translating polysome complexes (6, 7, 10–12, 14, 19), one might predict priming of the intrinsic host defense responses (e.g., RNA interference [RNAi], nonsense-mediated RNA decay, nucleic acid sensors) relative to a homogeneous viral RNA population with intact replication/translation signals.…”

“…In the 1970s, PMV was found to be the associated causal agent of St. Augustine decline disease of St. Augustinegrass (Stenotaphrum secundatum) (Fig. 1B) and has recently reemerged as the predominant viral pathogen of bioenergy switchgrass (Panicum virgatum) (25–27). Within an infected cell, PMV frequently supports the replication of distinct subviral agents, including a satellite virus (SPMV) with a 0.8-kb genome and 0.3- to 0.5-kb satellite RNA populations (Fig.…”

Brachypodium and plant viruses: entwined tools for discovery

“…Importantly, in a survey of viruses in switchgrass, mixed infections were not uncommon. In fact, virus ( n +1) infections were in combinations not previously reported, primarily with PMV (and SPMV and satRNAs), plus aphid‐transmitted viruses (CYDV, BYDV and SCMV) (Stewart et al , ; Pyle & Scholthof, ). Similarly, single infections as well as sequential infections with aphid‐transmitted BYDV and seed‐borne BSMV (and vice versa) differ when measuring virus titer, virulence and seed yield; these effects are likely to be indicative of virus–virus successes in nature (Marchetto & Power, ) and outcomes that can be evaluated with NGS data and the identification of asymptomatic viruses and virus effects on abiotic stress tolerance.…”

“…Co‐infection systems using Barley yellow dwarf virus (BYDV; luteovirus) and Cereal yellow dwarf virus (CYDV; polerovirus), which frequently trans‐encapsidate their genomic RNAs, open further avenues to determine the role of two or more viruses in the relative fitness of each virus (replication, movement, transmission). A more complex example for future investigation could be study of host–virus ( n +1) interactions between PMV (complex) and BYDV/CYDV in switchgrass (Stewart et al , ) and in the laboratory using Brachypodium; BYDV infects Brachypodium via an aphid vector (Tao et al , ).…”