Effect of Puccinia silphii on Yield Components and Leaf Physiology in Silphium integrifolium: Lessons for the Domestication of a Perennial Oilseed Crop

Disease resistance gene count increases with rainfall in Silphium integrifolium

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.

Assessing effective mechanical and chemical strategies for managing Eucosma giganteana (Lepidoptera: Tortricidae) in the perennial oilseed crop, Silphium integrifolium (Asteraceae: Heliantheae)

Eucosma giganteana (Riley) is a native specialist pest of silflower, Silphium integrifolium Michx., which is currently being domesticated as a perennial oilseeds crop. The larvae of this moth attack silflower capitula and root crowns, causing both seed damage and long-term degradation of plants. To determine methods to manage E. giganteana in silflower crop fields, we conducted a laboratory bioassay and 3 field experiments to assess the effects of a suite of organic, conventional, and mechanical treatments on E. giganteana mortality and colonization of flower heads. Pyrethroids (permethrin, cyfluthrin), chlorantraniliprole, and methoxyfenozide each had significant insecticidal effects on E. giganteana in at least 2 of the experiments conducted. Nematodes marginally increased larva mortality in the laboratory bioassay and could be further investigated as a soil-applied biological control. In 2 separate field experiments, trimming the top 15% of silflower plants to delay flowering did not alone reduce E. giganteana colonization of flower heads throughout the growing season. However, when trimming was paired with a single chlorantraniliprole application, colonization of capitula was reduced by 83% over untreated control plants. Collectively, these experiments provide evidence for several treatments that could be further tested and incorporated into an integrated pest management strategy for E. giganteana.

Unpredicted, rapid and unintended structural and functional changes occurred during early domestication of Silphium integrifolium, a perennial oilseed

MAIN CONCLUSION

Selection for increased yield changed structure, physiology and overall resource-use strategy from conservative towards acquisitive leaves. Alternative criteria can be considered, to increase yield with less potentially negative traits. We compared the morphology, anatomy and physiology of wild and semi-domesticated (SD) accessions of Silphium integrifolium (Asteraceae), in multi-year experiments. We hypothesized that several cycles of selection for seed-yield would result in acquisitive leaves, including changes predicted by the leaf economic spectrum. Early-selection indirectly resulted in leaf structural and functional changes. Leaf anatomy changed, increasing mesophyll conductance and the size of xylem vessels and mesophyll cells increased. Leaves of SD plants were larger, heavier, with lower stomatal conductance, lower internal CO₂ concentration, and lower resin concentration than those of wild types. Despite increased water use efficiency, SD plants transpired 25% more because their increase in leaf area. Unintended and undesired changes in functional plant traits could quickly become fixed during domestication, shortening the lifespan and increasing resource consumption of the crop as well as having consequences in the provision and regulation of ecosystem services.

Field Trapping and Flight Capacity of Eucosma giganteana (Riley) (Lepidoptera: Tortricidae) in Response to Behaviorally Active Congeneric Semiochemicals in Novel Silflower Agroecosystems

Silphium integrifolium is a novel perennial crop being developed for oilseed and biofuel in the midwestern US. One of the primary pests in this system is Eucosma giganteana (Lepidoptera: Tortricidae). Little is known about the chemical ecology or flight behavior of E. giganteana, but many semiochemicals have been identified from other closely related Eucosma species. Some of these compounds include: (Z)- and (E)-8-dodecenyl acetate, (E)-9-dodecenyl acetate, (Z)-8-dodecenol, (E,E)-8,10-dodecadienyl acetate, and (Z,E)-9,12-tetradecadienyl acetate. The goals of this study were to evaluate whether any of these compounds could improve capture of E. giganteana on clear sticky cards in the field, and the most attractive volatiles might affect flight behavior on a computer-automated flight mill assay. We found that there was significant attraction to (E)-8-dodecenyl acetate in two years in the field, which may possibly be a component in the pheromone blend for E. giganteana. On flight mills, E. giganteana flew an average of 23 km in a 24 h period. The presence of attractive stimuli (e.g., (E)-8-dodecenyl acetate) had arresting properties and decreasing flight distance on the mill by 78 to 80%. The longest flight distances were registered in the morning (4:00-12:00) and were 1.8-fold greater than flight distances and durations at night (20:00-4:00). (E)-8-dodecenyl acetate may be useful in behaviorally based monitoring and management strategies for E. giganteana. Overall, our research expands the knowledge on the chemical ecology of adult E. giganteana.

Abiotic and biotic context dependency of perennial crop yield

Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass-Thinopyrum intermedium-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (Silphium intregrifolium), and alfalfa (Medicago sativa). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both Silphium and alfalfa strongly benefited from AM fungi. The presence of native prairie AM fungi had a greater benefit to Silphium in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of Silphium and alfalfa. This study identifies the importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.

New Food Crop Domestication in the Age of Gene Editing: Genetic, Agronomic and Cultural Change Remain Co-evolutionarily Entangled

The classic domestication scenario for grains and fruits has been portrayed as the lucky fixation of major-effect "domestication genes." Characterization of these genes plus recent improvements in generating novel alleles (e.g., by gene editing) have created great interest in de novo domestication of new crops from wild species. While new gene editing technologies may accelerate some genetic aspects of domestication, we caution that de novo domestication should be understood as an iterative process rather than a singular event. Changes in human social preferences and relationships and ongoing agronomic innovation, along with broad genetic changes, may be foundational. Allele frequency changes at many loci controlling quantitative traits not normally included in the domestication syndrome may be required to achieve sufficient yield, quality, defense, and broad adaptation. The environments, practices and tools developed and maintained by farmers and researchers over generations contribute to crop yield and success, yet those may not be appropriate for new crops without a history of agronomy. New crops must compete with crops that benefit from long-standing participation in human cultural evolution; adoption of new crops may require accelerating the evolution of new crops' culinary and cultural significance, the emergence of markets and trade, and the formation and support of agricultural and scholarly institutions. We provide a practical framework that highlights and integrates these genetic, agronomic, and cultural drivers of change to conceptualize de novo domestication for communities of new crop domesticators, growers and consumers. Major gene-focused domestication may be valuable in creating allele variants that are critical to domestication but will not alone result in widespread and ongoing cultivation of new crops. Gene editing does not bypass or diminish the need for classical breeding, ethnobotanical and horticultural knowledge, local agronomy and crop protection research and extension, farmer participation, and social and cultural research and outreach. To realize the ecological and social benefits that a new era of de novo domestication could offer, we call on funding agencies, proposal reviewers and authors, and research communities to value and support these disciplines and approaches as essential to the success of the breakthroughs that are expected from gene editing techniques.