Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant’s source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

All figures and code were generated in RStudio 2022.02.3+492 "Prairie Trillium" Release. All packages needed to run the R code are shown in the RMD’s. Code to generate figures and statistical analysis: DVTindex_help.Rmd Code to generate figure 3 Figure5_PrairieVSCommonGarden Code to generate figure 5 PATHOFigs_for_Manu_FEB22.Rmd Code to generate figures 1, 2, 4 SUPP_Figure3_DimPathoEDIT.Rmd Code to generate supplementary figure 3 (fig S3) STATSAnalysis_PathoDim2B.Rmd Code to generate all tables and statistical analysis in the manuscript Description of data files: 2019and2020Prairie_data.txt This file contains data collected from the prairie sites in 2019 and 2020 Dim2b_latlon.csv The latitudinal and longitudinal coordinates for the common garden sites and prairie sites as well as precipitation data DVTINDEX_from_DVT.csv A separate file that contains the data that produced fig 3. This data file is sourced from SEPT2019_2020_COMPILED_2b_DATACOLL.txt SEPT2019_2020_COMPILED_2b_DATACOLL.txt SEPT2019_2020_COMPILED_2b_DATACOLL_plots.txt SEPT2019_2020_COMPILED_2b_DATACOLL_plots_longversion.txt These 3 data files are different versions of the same raw data that was collected from the common garden sites in 2019 and 2020. The code calls for all 3 at different points to generate plots and run statistical analyses Summary [ insert unique name here] Various data frames generated from r mark downs that contain summary statistics of the data. These are used to produce the figures in PATHOFigs_for_Manu_FEB22.Rmd graphs.

Ongoing domestication of whole-leaf rosinweed, Silphium integrifolium Michx., as a perennial oilseed and forage crop aims to increase yields while limiting decreases in other desirable traits (i.e., trade-offs). Two changes to plant architecture, increasing pistillate ray florets head(-1) ( = feminization) and reduced lateral branching of stems, have been considered for their potential to improve oil yields but with limited understanding of potential trade-offs. Field tests with genets that vary for feminization failed to show that increasing the number of female florets head(-1) had any effect on pollinator visitation and seed set (%) but revealed that feminization reduced embryo mass achene(-1). In general, tripling the number of ray florets head(-1) reduced the mass of individual embryos by 50% or more, which suggests feminization still provides a net benefit for oil yields. Clipping (bud removal) used to simulate reduced branching in S. integrifolium affected components of yield in ways that were generally predictable; heads (receptacles) became larger and mass achene(-1) increased. However, the large number of buds removed to achieve modest increases in head size and achene mass make reduced branching appear undesirable. Ultimately, S. integrifolium genets with genetically reduced branching are needed to make the best evaluation of this potential change. Both sets of experiments reveal plasticity in S. integrifolium yield components and suggest that efforts to improve the quality of phenotypic data are important to efficient selection.

Silflower (Silphium integrifolium (Michaux)) is a native North American relative of sunflower that is undergoing domestication as a perennial oilseed crop. As silflower incurs pest damage from multiple insect species, it is necessary to screen genotypes for their effect on insect performance such that more pest tolerant/resistant accessions can be incorporated into future silflower breeding programs. We present a bioassay protocol for silflower using the generalist herbivore fall armyworm (Spodoptera frugiperda (J. E. Smith)). In this study, fall armyworm larvae were placed on leaf and flower tissue from eleven silflower genotypes, one cup plant (Silphium perfoliatum (L.) (Asterales: Asteraceae)) genotype, and an inbred sunflower line (Helianthus annuus (L.) (Asterales: Asteraceae), HA89). Caterpillar weight gained during a 4-d feeding period significantly differed on leaf and floral tissue from different silflower genotypes, between the Silphium species (silflower and cup plant), and between Silphium genotypes and annual sunflower. Two wild silflower genotypes produced lower larval weight gain on both the floral and leaf tissue than all other genotypes, suggesting these genotypes have either lower nutrition or greater resistance to fall armyworm. However, nonsignificant correlations between larval growth on floral versus leaf tissue across all plant species tested and among all silflower accessions suggest insect performances on these tissue types in silflower are independent. Along with identifying germplasm of interest for silflower breeding programs, we established an easily replicable bioassay protocol using fall armyworm on silflower floral and leaf tissues.

Silflower (Silphium integrifolium Michx.) is in the early stages of domestication as a perennial version of oilseed sunflower, its close relative. Grain crops with deep perennial root systems will provide farmers with new alternatives for managing soil moisture and limiting or remediating soil erosion, fertilizer leaching, and loss of soil biota. Several cycles of selection for increased seed production potential following initial germplasm evaluation in 2002 have provided opportunities to document the botany and ecology of this relatively obscure species, to compare agronomic practices for improving its propagation and management, and to evaluate the differences between semi-domesticated and wild accessions that have accrued over this time through intentional and unintentional genetic processes. Key findings include: domestication has increased aboveground biomass at seedling and adult stages; seed yield has increased more, achieving modest improvement in harvest index. Harvest index decreases with nitrogen fertilization. Silflower acquires nitrogen and water from greater depth than typical crops. In agricultural silflower stands within its native range, we found that Puccinia silphii (rust) and Eucosma giganteana (moth) populations build up to unacceptable levels, but we also found genetic variation for traits contributing to resistance or tolerance. Breeding or management for reduced height and vegetative plasticity should be top priorities for future silflower research outside its native range.