To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was subjected to paired-end Illumina sequencing at ∼9 × depth and evaluated for several agronomic traits. We discovered 240.2 million single nucleotide polymorphisms (SNPs) after alignment to the Morex V3 assembly and 24.4 million short (1 to 50 bp) insertions and deletions. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1H close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for seedling stem rust resistance, including 2 novel loci on chromosomes 1H and 6H and one co-locating to the complex RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

An emerging paradigm in public health focuses on enhancing nutrition in existing food staples to reduce chronic disease at the population scale, rather than relying on individuals to change their behavior. This paradigm leverages plant and animal breeding, production practices, and processing to enhance nutrition, whereby foods consumed by millions can be improved at low incremental cost. This article supports and operationalizes this paradigm, illustrating the potential to improve diets through a case study that increases the arabinoxylan fiber content of commodity wheat through classical plant breeding (a non-GMO technology). The approach described in this article proposes to link agricultural and food science with health system implementation to deliver equitable access, improved healthcare outcomes and cost savings, and improved community health. Based on published dose-response relationships, comparative risk modeling indicates that modest fiber increases achieved by the commodity wheat breeding led to reduced population-level risks of 1-3% for cardiovascular disease, 3-4.5% for type 2 diabetes, and 1-3.5% for colorectal cancer, translating into substantial healthcare cost savings when implemented at a national scale. This article outlines possible low-risk pathways for implementing these nutrition increases at the population scale through commodity supply chains and community-level nutrition improvement efforts and evaluates the ranges of potential population-level impacts.

Pests and pathogens contribute to substantial crop yield losses, and these losses are predicted to be exacerbated by varying and new pest pressures associated with climate change. As such, characterizing variation in immune responses is critical for developing new plant breeding approaches for multiple biotic stress resilience. We thus tested the extent to which plants vary in responsiveness to defense elicitation and associated growth-defense trade-offs, and how these responses depended on field and pathogen conditions. Using a panel of >250 spring oat (Avena sativa L.) genotypes, we evaluated phenotypic and genetic variation in defense elicitation by measuring avenanthramides, specialized defensive metabolites, and disease resistance, as well as yield and growth traits. We found that defense elicitation increased the concentration of defensive avenanthramides across trials, and reduced the severity of crown rust and Fusarium head blight. There was substantial genetic variation in responses, and also genotype-by-elicitation state interactions in field trials. While plant growth was reduced in some trials, there were no loci identified by genome-wide association mapping for either growth or defense regulation. These results demonstrate that targeting variation in regulation of defense can contribute to breeding for resilient crops, and that breeders could develop genotypes with reduced growth-defense trade-offs.

The socioeconomic value of content presented at the ASA‐CSSA‐SSSA (where ASA‐CSSA‐SSSA is American Society of Agronomy–Crop Science Society of America–Soil Science Society of America) Annual Meetings from 2014 to 2023 is estimated at $64.2 billion and is presented in this commentary as a thought exercise, highlighting the potential scale of research dissemination in scientific meetings. Scientific meetings are instrumental for propelling the quality and advancement of research via fostering timely feedback, knowledge dissemination, fresh perspectives, stimulation for networking and new collaborations, preparing scientists for public engagement, and addressing contemporary challenges of cultural accessibility and opportunity. Additionally, the broader impacts include near‐term benefits to agricultural and environmental scientists that can transform careers and perspectives on the world, especially for students and early career members. The benefits from these impacts on scientists are then anticipated to propagate into broader and longer term positive impacts on humanity worldwide. In this commentary, we offer the above as a provocation to spark peer discussion on evaluating scientific meetings’ contributions, alongside a working list of broader impacts to inspire philosophical and methodological innovations for quantifying their value.

Foliar diseases of winter malting barley (Hordeum vulgare) include scald (Rhynchosporium commune), Stagonospora nodorum blotch (Parastagonospora nodorum), spot blotch (Bipolaris sorokiniana), and net blotch (Pyrenophora teres). Symptoms include water-soaked to necrotic lesions with a distinctive brown margin (scald); yellowish to tan-brown, oval or lens-shaped lesions (Stagonospora nodorum blotch); small circular dark brown lesions with a chlorotic zone (spot blotch and spot form net blotch); and small dark brown lesions that develop into a net-like pattern (net form net blotch). This report evaluates a collection of 8 cultivars and 28 breeding lines for reaction to the foliar diseases. The trial was conducted in two field sites in Tompkins County near Ithaca, NY, in 2024. Results indicate differentiation of reaction to natural inoculum of the foliar diseases and identified lines with resistance to scald, Stagonospora nodorum blotch, and net/spot blotches that may be useful for breeding for foliar disease resistance.

Small grains provide agronomic benefits that are critical to the success of organic production, and opportunities within local food movements create expanded markets for small grains. However, diversifying rotations with small grains can present challenges related to production, infrastructure, and markets. Here, we draw upon over two decades of integrated research and Extension efforts to support organic small grain production in the Upper Midwest, Northeast, and other regions of the United States where these crops are underutilized. Lessons learned have led to the development of guiding principles for a systems-level approach to support regional organic small grain production. Forming innovative partnerships between farmers, researchers, and end users is critical. This enables research, production, and markets to adjust to local needs, adapt to available infrastructure, and foster local grain economies. The key research challenges that lie ahead are also discussed, especially adapting organic grain production practices to regional conditions and changing climates. The systems-level approach to organic small grain research highlighted here will increase the success and resilience of organic farms across the United States and expand the adoption of organic small grain production. Local food movements are creating markets for small grains that provide opportunities for organic farmers. Growing small grains provides agronomic benefits that are critical to successful organic field crop production. Production challenges include lack of local infrastructure, adapting to local climate, and local market demands. A systems-level approach of regional partnerships between farmers, researchers, and end users enables farm success. Research must continue to adapt organic grain production practices to regional conditions and changing climates.

The dispersion of plant pathogens, such as rust spores, is responsible for more than 20% of global crop yield loss annually. However, the release mechanism of pathogens from flexible plant surfaces into the canopy is not well understood. In this study, we investigated the interplay between leaf elasticity and rainfall, revealing how a flexible leaf structure can generate a lateral flow stream, with embedded coherent structures that enhance transport. We first modeled the linear coupling between drop momentum, leaf vibration, and the stream flux from leaf surfaces. With Lagrangian diagnostics, we further mapped out the nested coherent structures around the fluttering profile, providing a dynamical description for local spore delivery. We hope the mechanistic details extracted here can facilitate the construction of physically informed analytical models for local crop disease management.

AbstractTransformative technologies such as artificial intelligence (AI) make difficult tasks more accessible and convenient. Since 2018, the use of AI in research has increased drastically, with annual publication rates of 3–5 times higher than pre‐2017. Currently, >100,000 manuscripts using AI are published annually within science and engineering, and >20,000 of these belong to the agricultural and environmental fields. Given the magnitude of use, clear communication on how AI is used and how it helps advance scientific knowledge is essential. Clear communication is perhaps more necessary with AI than previous technologies due to its broad and flexible spectrum of uses, the “black‐box” nature of deep‐learning algorithms, and ongoing debates regarding AI's predictive power versus knowledge of first‐principles mechanistic and process‐based theories and models. In this commentary, we provide guidelines and discussion points to the scientific community to ensure transparent and effective communication of AI research in agricultural and environmental research publications.

The modeling of genotype x environment interactions (GEI) is important to understand how new crops perform in different environments and management systems. Naked barley (Hordeum vulgare L.) is a type of barley where the hull threshes freely from the grain and can be used for multiple end uses, including food, malt, and animal feed. We examined the performance of a winter naked barley trial grown in organic conditions across three regions and 3 years in northern latitude regions of the United States. We recorded yield, test weight, heading date, plant height, threshability, winter survival, barley stripe rust (Puccinia striiformis f. sp. hordei Westend), barley scald (Rhynchosporium commune Zaffarano, McDonald and Linde sp. nov), and spot blotch (Cochliobolus sativus, anamorph Bipolaris sorokiniana (S. Ito & Kurib.). Barley stripe rust, plant height, heading date, preharvest sprouting, and threshability had high heritability and low GEI. Grain yield, test weight, scald, and winter survival had high GEI and were analyzed using the additive main effect and multiplicative interaction (AMMI) model, genotype plus GEI biplot (GGE), and Finlay-Wilkinson (FW) stability analysis. The environmental patterns explained by the AMMI and GGE models indicated that selection for high GEI traits should occur within target environments and across multiple years within the target environments. Environmental groups were separated by Oregon as the first group and Wisconsin and New York as the second group. Barley stripe rust, plant height, heading date, preharvest sprouting, and threshability had high heritability and low genotype x environment interactions. Grain yield, test weight, scald, and winter survival had high genotype x environment interaction effects. Environmental groupings were separated into OR as the first group and NY and WI as the second group.

Foliar fungal diseases are a major limitation in organic naked barley (Hordeum vulgare L.) production. The lack of conventional fungicides in organic systems increases reliance on genetic resistance. We evaluated the severity of barley stripe rust (Puccinia striiformis f. sp. hordei Westend), leaf rust (Puccina hordei sp. hordei), spot blotch (Cochliobolus sativus, anamorph Bipolaris sorokiniana (S. Ito & Kurib.) Drechsler ex Dastur), and scald (Rhynchosporium commune Zaffarano, McDonald and Linde sp. nov) on a naked barley diversity panel of 350 genotypes grown in 13 environments to identify quantitative trait loci associated with disease resistance. Genome-wide association analyses across and within environments found 10 marker trait associations for barley stripe rust, four marker trait associations for leaf rust, one marker trait association for scald, and five marker trait associations for spot blotch. Structure analysis identified six Ward groups based on genotypic diversity. Resistance to susceptible allele ratios were high for stripe rust and spot blotch, moderate for leaf rust, and low for scald. Combined phenotypic analysis values for each disease overlayed by a principal component analysis found distinct resistance and susceptibility patterns for barley stripe rust and scald. Most significant marker trait associations were previously identified in the literature, providing confirmation and potential new sources of disease resistance for genetic improvement of naked barley germplasm.

Malt for craft “all-malt” brewing can have high quality, PHS resistance, and malted in normal timeframes. Canadian style adjunct malt is associated with PHS susceptibility. Expansion of malting barley production into non-traditional growing regions and erratic weather has increased the demand for preharvest sprouting (PHS) resistant, high quality malting barley cultivars. This is hindered by the relatively unknown relationships between PHS resistance and malting quality. Here we present a three-year study of malting quality and germination at different after-ripening durations post physiological maturity. Malting quality traits alpha amylase (AA) and free amino nitrogen (FAN) and germination rate at six days post PM shared a common association with a SNP in HvMKK3 on chromosome 5H in the Seed Dormancy 2 (SD2) region responsible for PHS susceptibility. Soluble protein (SP) and soluble over total protein (S/T) both shared a common association with a marker in the SD2 region. Significant genetic correlations between PHS resistance and the malting quality traits AA, FAN, SP, S/T were detected across and within HvMKK3 allele groups. High adjunct malt quality was related to PHS susceptibility. Selection for PHS resistance led to a correlated response in malting quality traits. Results strongly suggest pleiotropy of HvMKK3 on malting quality traits and that the classic “Canadian-style” malt is caused by a PHS susceptible allele of HvMKK3. PHS susceptibility appears to benefit the production of malt intended for adjunct brewing, while PHS resistance is compatible with all-malt brewing specifications. Here we present our analysis on the effect of combining complexly inherited and correlated traits with contrasting goals to inform breeding practice in malting barley, the general principles of which can be extended to other breeding programs.

Abstract Background During sepsis, neutrophils, upon activation, undergo biophysical and biochemical changes that may terminate in the release of neutrophil extracellular traps (NETs) (1–3). The IntelliSep test is a rapid sepsis diagnostic that assesses immune activation by quantifying biophysical properties of leukocytes from whole blood in <10 minutes. The test results in the IntelliSep Index (ISI), ranging between 0.1–10.0, stratified into three interpretation bands (Band 1, Band 2, and Band 3) based on the probability of the clinical syndrome of sepsis (4, 5). We investigated the correlation between the IntelliSep result and immunological changes observed during leukocyte activation through in-vitro studies and using clinical samples from non-septic and septic patients. Methods In-vitro Studies: Healthy blood samples were collected between April - August 2022 from 18 volunteers at a blood donor center. Aliquots of each blood sample were incubated for 10 minutes with phorbol myristate acetate (PMA) in phosphate-buffered saline at one of 3 concentrations: 0, 200, and 400 nM prior to the IntelliSep test (3 repeats per donor per concentration). Clinical Studies: Subjects with signs or symptoms of infection were enrolled from Emergency Departments (EDs) in three similar but distinct prospective cohort studies (February 2016—September 2019) (1, 2). The IntelliSep test was performed on a aliquot of fresh whole blood from each subject, and remnant plasma was prepared and frozen for later analysis. Plasma levels of neutrophil elastase-DNA (NE DNA) and citrullinated histone H3-DNA (Cit-H3 DNA) complexes were quantified using previously reported custom ELISAs 3,6. Subjects were retrospectively adjudicated as sick (adjudicated as septic with SOFA scores peaking on the day of enrollment compared to two subsequent days) and “healthy” (SOFA for day of enrollment <2, hospital length of stay <3 days). Results Significant increases in ISI scores were observed with increasing concentration of PMA in healthy blood samples (0 and 200: P < 10−10; 0 and 400: P < 10−10). The clinical analysis cohort consisted of 39 “sick” and 42 “healthy” subjects. Linear correlation was observed between the ISI and NE DNA and Cit-H3 DNA quantities with significant increases across ISI Interpretation Bands (Band 1 to Band 3: P < 0.001). Conclusion Correlation of increasing ISI and PMA concentration supports the hypothesis that the biophysical changes measured by the IntelliSep test result from leukocyte activation. Observed correlation between the ISI and NET quantities suggest that NET formation is one of the activation pathways that result in the biophysical changes measured in the ISI. Together these experiments support that biophysical changes of leukocyte activation measured using a cellular host response test could provide a window into a patient’s state of dysregulated immunity and may have the potential to aid ED physicians in timely diagnosis of sepsis.

Threshability, defined here as the propensity of grains to lose their hull after harvest, is a key trait in naked barley (Hordeum vulgare L.). While threshability is a defining characteristic of naked grains and has been found to be associated with grain size and shape, its genetic architecture is poorly described. The goals of this study were to identify quantitative trait loci associated with threshability and evaluate their utility as covariates in genomic prediction models. A genome-wide association study identified two loci on chromosomes 2H and 3H associated with threshability. The locus on chromosome 2H accounted for 9.9% of the phenotypic variance explained (PVE). The locus on chromosomes 3H accounted for 7.8% of the PVE. With effects on threshability of 0.18 and 0.29 for each marker, respectively, these markers could have a limited impact when implemented in marker-assisted selection. Predictive ability for threshability was 0.842 using a structured genomic best linear unbiased prediction model. Incorporation of the markers with significant associations as covariates in the model did not improve predictive ability. Predictive ability was improved by the use of a multi-trait model including grain test weight. The high predictive ability for threshability overall indicate that genomic selection would be useful in selection for threshability in naked barley.

Selection for more nutritious crop plants is an important goal of plant breeding to improve food quality and contribute to human health outcomes. While there are efforts to integrate genomic prediction to accelerate breeding progress, an ongoing challenge is identifying strategies to improve accuracy when predicting within biparental populations in breeding programs. We tested multiple genomic prediction methods for 12 seed fatty acid content traits in oat (Avena sativa L.), as unsaturated fatty acids are a key nutritional trait in oat. Using two well-characterized oat germplasm panels and other biparental families as training populations, we predicted family mean and individual values within families. Genomic prediction of family mean exceeded a mean accuracy of 0.40 and 0.80 using an unrelated and related germplasm panel, respectively, where the related germplasm panel outperformed prediction based on phenotypic means (0.54). Within family prediction accuracy was more variable: training on the related germplasm had higher accuracy than the unrelated panel (0.14-0.16 and 0.05-0.07, respectively), but variability between families was not easily predicted by parent relatedness, segregation of a locus detected by a genome-wide association study in the panel, or other characteristics. When using other families as training populations, prediction accuracies were comparable to the related germplasm panel (0.11-0.23), and families that had half-sib families in the training set had higher prediction accuracy than those that did not. Overall, this work provides an example of genomic prediction of family means and within biparental families for an important nutritional trait and suggests that using related germplasm panels as training populations can be effective.

AbstractIn order to produce successful varieties, wheat breeding programs must develop several strategies that fall under one of the following topics: line development, population improvement, and selection methods. This chapter focuses on breeding activities related to population improvement and selection methods, while Chap. 5 discusses line development. The objective of population improvement is to enhance the entire genetic base of the breeding program, while selection methods aim to identify breeding lines with superior potential or performance. As with line development approaches, numerous population improvement and selection methods have been developed in order to enhance breeding program efficiency and achieve genetic improvement. This chapter will provide an overview of population improvement and selection methods in the context of wheat breeding, discuss their advantages and disadvantages, and summarize empirical studies that have evaluated them in order to inform breeding program design.

To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 93% imputation accuracy with 0.01x sequence coverage, which was only slightly lower than the accuracy obtained using the 0.5x sequence coverage (96.9%). Compared to Beagle, on average, PHG imputation was ~4% (p-value = 0.00027) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. The reduced accuracy of imputation with GBS data (90.4%) is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequlibrium and proportion of identity-by-descent regions among accessions in our reference panel. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.

Meiotic recombination is a source of allelic diversity, but the low frequency and biased distribution of crossovers that occur during meiosis limits the genetic variation available to plant breeders. Simulation studies previously identified that increased recombination frequency can retain more genetic variation and drive greater genetic gains than wildtype recombination. Our study was motivated by the need to define desirable recombination intervals in regions of the genome with fewer crossovers. We hypothesized that deleterious variants, which can negatively impact phenotypes and occur at higher frequencies in low recombining regions where they are linked in repulsion with favorable loci, may offer a signal for positioning shifts of recombination distributions. Genomic selection breeding simulation models based on empirical wheat data were developed to evaluate increased recombination frequency and changing recombination distribution on response to selection. Comparing high and low values for a range of simulation parameters identified that few combinations retained greater genetic variation and fewer still achieved higher genetic gain than wildtype. More recombination was associated with loss of genomic prediction accuracy, which outweighed the benefits of disrupting repulsion linkages. Irrespective of recombination frequency or distribution and deleterious variant annotation, enhanced response to selection under increased recombination required polygenic trait architecture, high heritability, an initial scenario of more repulsion than coupling linkages, and greater than 6 cycles of genomic selection. Altogether, the outcomes of this research discourage a controlled recombination approach to genomic selection in wheat as a more efficient path to retaining genetic variation and increasing genetic gains compared with existing breeding methods.

There is an increased demand for food-grade grains grown sustainably. Hard red winter wheat has comparative advantages for organic farm rotations due to fall soil cover, weed competition, and grain yields. However, limitations of currently available cultivars such as poor disease resistance, winter hardiness, and baking quality, challenges its adoption and use. Our goal was to develop a participatory hard red winter wheat breeding program for the US Upper Midwest involving farmers, millers, and bakers. Specifically, our goals include (1) an evaluation of genotype-by-environment interaction (GEI) and genotypic stability for both agronomic and quality traits, and (2) the development of on-farm trials as well as baking and sensory evaluations of genotypes to include farmers, millers, and bakers' perspectives in the breeding process. Selection in early generations for diseases and protein content was followed by multi-environment evaluations for agronomic, disease, and quality traits in three locations during five years, on-farm evaluations, baking trials, and sensory evaluations. GEI was substantial for most traits, but no repeatable environmental conditions were significant contributors to GEI making selection for stability a critical trait. Breeding lines had similar performance in on-station and on-farm trials compared to commercial checks, but some breeding lines were more stable than the checks for agronomic, quality traits, and baking performance. These results suggest that stable lines can be developed using a participatory breeding approach under organic management. Crop improvement explicitly targeting sustainable agriculture practices for selection with farm to table participatory perspectives are critical to achieve long-term sustainable crop production. Key message We describe a hard red winter wheat breeding program focused on developing genotypes adapted to organic systems in the US Upper Midwest for high-end artisan baking quality using participatory approaches.