Steven R. Scofield

It is essential to evaluate the effectiveness of breeding programs to ensure they continue to deliver value to stakeholders, including farmers, millers, and consumers. We evaluated the performance of the University of Illinois Oat Breeding Program (UIOBP) by quantifying realized genetic trends for key agronomic, grain quality, and disease resistance traits. Additionally, we assessed the effect of heat stress and genetic diversity to inform future breeding decisions. Our analysis integrated genotypic, pedigree, historical weather, and phenotypic data collected over an 18‐year period from 2002 to 2019. Genetic trends were estimated using mixed models and the control population method. We quantified genetic correlations, rates of genetic gain, and the effects of temperature on yield and test weight, and assessed genetic diversity using molecular marker data, pedigree reconstruction, and population structure. Significant genetic trends were observed for yield (35.8 kg ha ^{− 1} year ^{− 1} ), test weight (0.63 g L ^{− 1} year ^{− 1} ), heading date (−0.01 days year ⁻¹ ), and plant height (−0.07 cm year ^{− 1} ), while barley yellow dwarf virus, groat content, and thins (%) showed no significant change. Genetic diversity analyses revealed weak population structure and slightly reduced effective population size in recent parental lines. Phenotypic analyses showed that high temperatures during critical reproductive periods reduced yield and test weight. The UIOBP has maintained genetic diversity while achieving favorable selection response in yield, test weight, heading time, and plant height; however, limited progress in milling traits highlights areas for improvement. These findings demonstrate the continued value of public oat breeding while informing future breeding efforts.

Since its initial detection in Indiana and Illinois in 2015, tar spot of maize, caused by Phyllachora maydis, has rapidly emerged as a significant constraint to maize ( Zea mays) production in the continental United States. Over the past decade, this pathogen has caused recurrent disease epidemics throughout maize-growing regions across the United States and Canada, causing substantial yield losses. Notably, in 2024, tar spot was responsible for an estimated economic yield loss of $1.37 billion to U.S. farmers. Despite its agronomic impact to U.S. agriculture, no definitive sources of genetic resistance to P. maydis have been identified in maize germplasm, underscoring a critical need to elucidate the molecular and genetic basis of disease resistance. Accordingly, recent studies have begun to investigate the genetic, molecular, and cellular mechanisms underlying P. maydis virulence and host colonization, with the long-term goal of developing durable resistance strategies. In this review, we synthesize the latest advances in our understanding of host–pathogen interactions within the maize– P. maydis pathosystem, with a focused emphasis on the genetic, molecular, and cellular dynamics that shape these interactions. Building on these insights, we outline key knowledge gaps and propose future research priorities aimed at accelerating the development of durable resistance and effective disease management strategies. Given the significant agricultural impact of P. maydis, coupled with its continued geographical expansion, we propose that this fungal pathogen poses an emerging threat to global maize production and emphasize the necessity for sustained research efforts to improve host resistance and disease management strategies. [ ] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.

We present a simple, efficient, and genotype-flexible method for transformation of small grain cereals. The method is named In-planta Agrobacterium-mediated cereal transformation or InPACT. We demonstrate the genotype flexibility of InPACT through successful transformation of 32 different wheat genotypes: 29 hexaploid (Triticum aestivum) and 3 tetraploid durum (Triticum durum) wheat accessions showing global adaptation. Experiments performed by experienced users and learners demonstrate that InPACT is highly reproducible, as both groups were able to generate transgenic wheat without difficulty. We further explored the utility of InPACT in other cereal crops and successfully transformed three barley (Hordeum vulgare), two oat (Avena sativa), and one rice (Oryza sativa) germplasm.

Key message: GWAS of 337 soft winter wheat genotypes from a breeding program in Indiana, USA identified marker-trait associations that likely correspond with existing and novel resistances to Septoria tritici blotch disease. Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici , is a major disease of wheat worldwide. To find additional sources of resistance, Genome-Wide Association (GWA) was used to analyze 337 soft winter wheat genotypes from Indiana, USA, by inoculating seedlings with two isolates of Z. tritici in a complete randomized design. Necrosis and pycnidia development were assessed at 14, 18 and 22 days post inoculation, enabling the calculation of area under the disease progress curve (AUDPC) for each parameter. Adjusted necrosis and pycnidia AUDPC scores were compared with 14,341 high-quality SNPs in a GWA analysis using the FarmCPU and GAPIT CMLM models to identify markers associated with the resistance. Significant (p < 0.05) isolate ξ genotype interactions were identified, confirming that the phenotypic variation was caused by isolate-specific resistance genes. Overall, 9 marker-trait associations (MTAs) were identified with Z. tritici necrosis and pycnidia resistance. All mapped MTAs were isolate and necrosis/pycnidia specific. Distinct MTAs were mapped for necrosis and pycnidia on chromosome 6A, and for pycnidia on chromosomes 1A, 1D, 4A, 7A, 3B and 5B. The MTAs on chromosomes 4A, 6A, 5B and 1D likely corresponded with the known genes Stb7 , Stb15 , Stb1 and Stb19 , respectively. Those on chromosomes 1A, 7A and 3B were not associated with previously known genes and may be novel. Candidate genes near the marker locations have been identified for further investigations. Indiana soft winter wheat germplasm segregates for novel and known Stb genes and constitutes a valuable breeding resource for Z. tritici resistance.

Most plant pathogens secrete effector proteins to circumvent host immune responses, thereby promoting pathogen virulence. One such pathogen is the fungus Fusarium graminearum, which causes Fusarium head blight (FHB) disease on wheat and barley. Transcriptomic analyses revealed that F. graminearum expresses many candidate effector proteins during early phases of the infection process, some of which are annotated as proteases. However, the contributions of these proteases to virulence remain poorly defined. Here, we characterize an F. graminearum endopeptidase, FgTPP1 (FGSG_11164), that is highly upregulated during wheat spikelet infection and is secreted from fungal cells. To elucidate the potential role of FgTPP1 in F. graminearum virulence, we generated FgTPP1 deletion mutants (Δ Fgtpp1) and performed FHB infection assays. Deletion of FgTPP1 reduced the virulence of F. graminearum as assessed by spikelet bleaching. Infection with wild-type F. graminearum induced full bleaching in about 50% of the spikes at 10 to 11 days postinfection, whereas this fraction was reduced to between 18 and 27% when using Δ Fgtpp1 mutants. Transient expression of green fluorescent protein-tagged FgTPP1 revealed that FgTPP1 localizes, in part, to chloroplasts and attenuates chitin-mediated activation of mitogen-activated protein kinase signaling, reactive oxygen species production, and cell death induced by an autoactive disease resistance protein when expressed in planta. Notably, the FgTPP1 protein is conserved across the Ascomycota phylum, suggesting that it may be a core effector among ascomycete plant pathogens. These properties make FgTPP1 an ideal candidate for decoy substrate engineering, with the goal of engineering resistance to FHB. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Wheat is one of the major sources of protein worldwide. Its hexaploidy significantly complicates the identification of genes that may be crucial for improving wheat production to meet the challenges of an increased world population and climate change. Virus-induced gene silencing (VIGS) using Barley stripe mosaic virus (BSMV)-based constructs has proven to be a very useful tool in the analysis of gene function in the hexaploid plant, wheat. However, most published applications of this technique focus on phenotypes that can be observed in the leaves of wheat. A few studies have reported successful VIGS in the spikes of wheat, but this has proven to be more difficult than the seedling leaf assays. This study reports a time course analysis of the movement of BSMV from the site of inoculation into the meristematic region of wheat. It also describes how the photobleaching phenotype resulting from silencing phytoene desaturase (PDS), which is often used as a reporter for VIGS, does not indicate the full extent of where VIGS occurs, and this can mislead scientists as they design silencing studies. These findings provide guidance for more effective VIGS studies to determine the function of genes expressed in the spikes of wheat and may be important for wheat improvement.

Phyllachora maydis is an ascomycete foliar fungal pathogen and the causal agent of tar spot in maize. Though P. maydis is considered one of the most economically important foliar pathogens of maize, our general knowledge of the trophic lifestyle and functional role of effector proteins from this fungal pathogen remains limited. Here, we utilized a genome-informed approach to predict the trophic lifestyle of P. maydis and functionally characterized a subset of candidate effectors from this fungal pathogen. Leveraging the most recent P. maydis genome annotation and the CATAStrophy pipeline, we show this fungal pathogen encodes a predicted Carbohydrate-active enzymes (CAZymes) repertoire consistent with that of biotrophs (monomertrophs). To investigate fungal pathogenicity, we selected eighteen candidate effector proteins that were previously shown to be expressed during primary disease development. We assessed whether these putative effectors share predicted structural similarity with other characterized fungal effectors and determined whether any suppress plant immune responses. Using AlphaFold2 and Foldseek, we showed one candidate effector, PM02_g1115, adopts a predicted protein structure similar to that of an effector from Verticillium dahlia . Furthermore, transient expression of candidate effector-fluorescent protein fusions in Nicotiana benthamiana revealed that most effector proteins localize to both the nucleus and the cytosol. Importantly, three candidate effectors consistently attenuated chitin-mediated reactive oxygen species production in N. benthamiana . Collectively, these results presented herein provide valuable insights into the predicted trophic lifestyle and putative functions of effectors from P. maydis and will likely stimulate continued research to elucidate the molecular mechanisms used by P. maydis to induce tar spot.

Fusarium head blight (FHB) is a devastating fungal disease of hexaploid wheat (Triticum aestivum). Several genetic loci were previously identified that control FHB resistance in wheat, including Fhb1. Fhb7, a major QTL conferring resistance to FHB, controlling for mycotoxin deoxynivalenol (DON) production, has been introgressed into soft red winter wheat (SRWW). As an exotic QTL, Fhb7 is associated with linkage drag, affecting agronomic and end-use quality performance. This study outlines a breeding strategy for introducing and pyramiding Fhb7 into SRWW breeding populations that already possessed Fhb1 and harbored some additional disease-resistance genes. In addition to the Fhb1-Fhb7 pyramiding, we developed gene-based markers for both genes and examined them on 57 SRWW breeding lines. Our data showed that 15 out of 57 breeding lines possessed both Fhb1 and Fhb7 resistant alleles. Two years of phenotypic data from the inoculated and misted irrigation field showed that the combination of Fhb1-Fhb7 lowers mycotoxin DON accumulation in kernels, which provides protection for end-users and the milling industry. The Fhb gene-pyramided lines, with the additional regionally important disease resistance genes, produced in this breeding pipeline showed reasonable agronomic traits and can be used in crossing programs for the widespread introgression in elite wheat cultivars.

Barley stripe mosaic virus (BSMV)-based vectors are frequently used in virus-induced gene silencing (VIGS) and, more recently, viral overexpression (VOX) studies in wheat. Two general strategies are employed to initiate infection in wheat plants with BSMV in VIGS and VOX studies. One method involves the direct infection of wheat using viral RNA produced via the in vitro transcription of BSMV constructs. The second class utilizes viral replication in an intermediate host plant to produce large amounts of BSMV viral particles that are then used to inoculate wheat plants. This study was designed to examine the potential for BSMV-VIGS constructs to rearrange during replication in the intermediate host and result in initiating the VIGS studies with a virus that is significantly different from the original experimental construct. It is shown that in the case of BSMV-VIGS constructs harboring a PDS-silencing fragment, significant rearrangement can occur during replication in the intermediate host that has the potential to introduce artifactual experimental outcomes.