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Data from: Emerging wild virus of native grass bioenergy feedstock is well established in the Midwestern USA and associated with premature stand senescence

Citation

Malmstrom, Carolyn M. et al. (2022), Data from: Emerging wild virus of native grass bioenergy feedstock is well established in the Midwestern USA and associated with premature stand senescence, Dryad, Dataset, https://doi.org/10.5061/dryad.bk3j9kddv

Abstract

This dataset includes values for the prevalence of switchgrass mosaic virus (Genus Marafivirus, Family Tymoviridae) detected with molecular diagnostics (RT-PCR) in individual Panicum virgatum (switchgrass) plants and in Graminella leafhoppers that feed on them. Surveys were conducted in 15 sites in August 2012. Stands surveyed had been established for some time and represent a range of landscape contexts. Measures of stand height and percent senescence were also collected. Land cover composition surrounding each site was calculated from the USDA-NASS Cropland Data Layer and estimates of drought impact were derived from the US Drought Monitor.

Methods

Field collections and laboratory analysis

Plant and leafhopper samples were collected in the field during the 2012 growing season. Virus infection was detected within samples using RT-PCR with specific primers. Detailed methods are described in the associated manuscript.

Land cover analysis

For land cover analysis, we evaluated relevant regions from the USDA National Agricultural Statistics Service Cropland Data Layer. 2012. Published crop-specific data layer [Online]. Available at https://nassgeodata.gmu.edu/CropScape/. USDA-NASS, Washington, DC.

Land cover types included within each aggregate category

We grouped all raster cells as belonging to one of the following eight broad land cover groups:

Agriculture: Alfalfa, Apples, Barley, Blueberries, Carrot, Cherries, Corn, Cucumber, Dry Beans, Grapes, Oats, Onion, Potatoes, Pumpkins (1.5 km only), Radish, Rye, Soybean, Squash, Sugarbeet, Sunflower, Watermelon (1.5km only), Winter Wheat
Barren: Barren
Forest: Deciduous Forest, Evergreen Forest, Mixed Forest
Grass/Meadow: Fallow Cropland, Grassland/Pasture, Other Hay, Sod/Grass Seed
Developed: Developed/High Intensity, Developed/Medium Intensity, Developed/Low Intensity, Developed/Open
Miscellaneous Perennial Habitat: Shrublands, Clover/Wildflowers
Open Water: Open Water
Wetlands: Herbaceous Wetland, Woody Wetlands

Following Werling et al., 2011 (Werling, B. P., T. D. Meehan, B. A. Robertson, C. Gratton, and D. A. Landis. 2011. Biocontrol potential varies with changes in biofuel-crop plant communities and landscape perenniality. Global Change Biology Bioenergy 3:347-359), we created an additional aggregate category, which contains elements from several categories above:

Herbaceous perennial habitat: Alfalfa, Other Hay, Fallow Cropland, Shrubland, Clover/Wildflowers, Grassland/Pasture

To quantify how much drought each study site experienced, we calculated a drought index value based on spatially-explicit estimates of the duration and weekly severity of drought conditions as published in the US Drought Monitor (https://droughtmonitor.unl.edu/). Description of methods as excerpted from our associated article: "The Drought Monitor rates moisture conditions as no drought or dryness (no drought rating), abnormally dry (D0), moderate drought (D1), severe drought (D2), extreme drought (D3), and exceptional drought (D4). For each site’s GPS location (i), we thus calculated a Drought Index (DI) as


where j = the growing season week, and dj = the Drought Monitor D value rating (0 – 4) for week j. Thus, weekly ratings of D0, D1, D2, D3, and D4 were valued as 1, 2, 3, 4, and 5 respectively. Weeks with no recorded drought or dryness were valued as 0. Switchgrass in this region typically sprout in early May, so we calculated DI for the 16 weeks from the week of May 1 through the week of August 14, when early August field measures were completed (i.e., n = 16)."

Usage Notes

Abbreviations used in field names (full descriptions of fields are provided in README file):

Samples were collected in two periods in August 2012. In field names, the first period (August 2-8 or early August) is referred to as 8a12 and the second period (Aug 23-29 or late August) as 8b12.

LH = leafhopper

prev = prevalence

gram = Graminella

aureo = G. aureovittata

oqmo = G. oquaka and G. mohri

PC = percent

Mn =mean

Data set

NA = missing data

Funding

National Institute for Agriculture, Award: 2011-67009-30137

U.S. Department of Energy, Award: DE-SC0018409

U.S. Department of Energy, Award: DE-FC02-07ER64494

National Science Foundation, Award: DEB 1832042

AgBioResearch, Michigan State University, Award: MICL02055

AgBioResearch, Michigan State University, Award: MICL02582

AgBioResearch, Michigan State University, Award: MICL02477