M. Kathryn Turner

Intermediate wheatgrass (IWG) [ Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] is a promising perennial grain candidate that The Land Institute has been directly domesticating since 2001. Grain from improved IWG can be sold under the trademark Kernza. Resistance to Fusarium head blight (FHB) is a high priority trait to reduce toxin content of the grain and protect the value and seed supply of Kernza. We evaluated two breeding cycles of IWG from 2018 to 2022 with each cycle containing ∼500 unique genets to investigate disease response and identify chromosomal regions associated with disease resistance. Quantitative trait loci were mapped for 17 different traits using 32,067 markers in 21 linkage groups with genome‐wide association analysis. A total of 188 unique marker‐trait associations were detected across 14 different traits with five of these traits related to FHB resistance. We additionally used the basic local alignment search tool alignment creation tool to identify homologies between the Fhb1 region of wheat and the IWG genome, including an IWG GDSL‐like lipase/Acylhydrolase gene (Thintv31194873.m.g) with similarity (query = 89%) to the Triticum aestivum Sumai 3 Fhb1 genomic sequence. Other candidate genes outside of the Fhb1 region were identified for Fusarium resistance with functions associated with toxin reduction and defense hormones and metabolites. These results provide loci that could be used in future selections to improve IWG's genetic resistance to FHB.

Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication.

Perennial groundcover (PGC) research is an expanding field of study focused on utilizing the soil‐protecting characteristics of perennial plants as permanent intercrops in row‐crop agriculture systems. However, there are some risks that PGC could serve as a “green bridge” between cash crops. Alfalfa mosaic virus (AMV) is one such disease that could infect legume PGCs, like kura clover (Trifolium ambiguum M. Bieb), and potentially be transmitted to cash‐crop companions (e.g., soybean). The objectives of the current study were to (i) evaluate AMV symptoms and susceptibility in kura clover and (ii) explore population structure and genetic diversity patterns utilizing simple sequence repeat markers across the United States Department of Agriculture National Germplasm Plant Service kura clover collection and various breeding populations from the University of Minnesota. Results showed that 96% tested kura clover field plants had AMV infection and the rate of seed transmission from parent to offspring was 0.4%. Genetic structure among kura clover germplasms generally revealed a ploidy‐based separation where diploid and hexaploid cytotypes from distinct genetic clusters and tetraploid germplasm manifest an intermediate pattern. The results indicated substantial AMV sensitivity among broadly based kura clover germplasm, and the risks of both yield losses and “green bridge” due to AMV infection in kura clover should be considered.

Perennial grains have been proposed as a soil-healthy alternative to annual grains. Intermediate wheatgrass (Thinopyrum intermedium), whose seed is currently sold under the trade name Kernza^®, and silflower (Silphium integrifolium), which is in the early stages of domestication at The Land Institute in Central Kansas, lack characterization for their deficiency symptoms. This has complicated attempts to assess the causes of visible stress on plants in the field and the greenhouse. By growing Th. intermedium and S. integrifolium in a set of hydroponic solutions, each containing all but one selected nutrient—including nitrogen, phosphorous, potassium, calcium, magnesium, sulfur, iron, boron, zinc, copper, molybdenum, and manganese—we were able to assess the effects of twelve different nutrient deficiencies across the two species. Visible symptoms were described and documented via photographs. The effects of the deficiencies on height, leaf biomass, root biomass, gas exchange and photosynthesis (silflower), and resin production (silflower) were measured. Calcium, nitrogen, and potassium were found to alter growth responses in intermediate wheatgrass; in silflower, growth, resin production, and photosynthetic traits were affected by many nutrient deficient treatments. Our results suggest that further work addressing how symptoms might look at the time of flowering, seed production, and in the field at different concentrations of key nutrients would help ongoing plant-breeding efforts.

Intermediate wheatgrass (IWG, Thinopyrum intermedium, (Host) Barkworth & D.R. Dewey subsp. intermedium, 2n = 6x = 42) is a novel perennial crop currently undergoing domestication efforts. It offers remarkable ecosystem services and yields higher relative to other perennial grain crops. While IWG is mostly resistant to Fusarium head blight (FHB), identifying genomic regions associated with resistance will help protect the crop from potential disease epidemics. An IWG biparental population of 108 individuals was developed by crossing parents differing in their response to FHB and bacterial leaf streak (BLS). The population was screened for disease reaction over three years using isolates collected from IWG plants in St. Paul, Minnesota, USA. Linkage maps representing the 21 IWG chromosomes were constructed from 4622 Single Nucleotide Polymorphism (SNP) markers, with one SNP at every 0.74 cM. Interval mapping identified 15 quantitative trait loci (QTL) associated with FHB resistance and 11 with BLS resistance. Models with two or three QTL combinations reduced FHB disease severity by up to 15%, and BLS by up to 17%. When markers associated with FHB resistance were used as cofactors in genomic selection models, trait predictive ability improved by 24–125%. These genomic regions and genetic markers associated with FHB and BLS resistance can also be used to safeguard annual cereal grains through gene introgression and selective breeding.

New crops with greater capacity for delivering ecosystem services are needed to increase agricultural sustainability. However, even in these crops, seed yield is usually the main criteria for grain domestication. This focus on yield can cause unintended structural and functional changes. Leaves of selected plants tend to be more vulnerable to infection, which can reduce performance, assimilates, and ultimately yield. Our objectives were to determine the impact of rust (caused by Puccinia silphii) on yield and leaf function in selected Silphium integrifolium (Asteraceae) plants. We tested the effect of a fungicide treatment on rust severity and yield, compared the rust infection of individuals in a population selected for yield, and related this to chemical changes at the leaf level. We also estimated heritability for rust resistance. We found that productivity indicators (head number and weight, leaf weight) and leaf processes (photosynthetic capacity, water use efficiency) were reduced when silphium leaves and stems were more heavily infected by P. silphii. Leaf resin content increased when susceptible plants were infected. Fungicide treatments were effective at reducing rust infection severity, but were ineffective at preventing yield losses. We propose that disease resistance should be included early in the selection process of new perennial crops.

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.

Two PCR-based assays were examined for tracing the presence of a Thinopyrum chromosome segment (Tc6 or Tc14) conferring barley yellow dwarf virus (BYDV) resistance in wheat breeding lines. The microsatellite gwm37 was used to assay the Thinopyrum chromosome segment or its wheat, Group 7, homoeologous segment, and was effective in characterising breeders material since heterozygous lines could be identified. A new set of primers derived from a Thinopyrum -specific DNA segment (csTiB1) provided a dominant marker that was readily scored by agarose gel electrophoresis. It was also demonstrated that the csTiB1 primers could be used to establish a solid phase PCR assay that avoided the requirement for gel electrophoresis and was amenable to use in a high-throughput, microtitre plate format. Depending on the number of DNA samples to be assayed, both primer pairs appear to have a place in breeding programs.