Matthew E. Hudson

The biochemical mechanisms by which virulent populations of soybean cyst nematode ( Heterodera glycines , SCN) overcome host resistance are critical to understanding this economically important pathogen. Here, we deployed metabolic and transcriptome profiling of soybean roots during the SCN infection and establishment process to investigate the molecular and biochemical mechanisms of pathogen establishment. Across samples from a time series spanning nematode invasion to syncytium maturation, we demonstrate that compatible SCN infection does not bypass host immunity but systematically remodels it. In a compatible interaction between soybean carrying the high-copy Rhg1 resistance locus challenged with HG Type 2.5.7 SCN virulent on this host, we identify a 72-metabolite defense signature spanning isoflavonoids, triterpenoid saponins, and phenylpropanoids that persist across all infection stages. Despite activation of this metabolic defense signature by the pathogen on infection, defense transcription is near silence by 3 days post-infection, while defense metabolites persist, revealing a critical decoupling of transcriptional and metabolic defense programs at the precise window of syncytium initiation. Suppression of phenylpropanoid accumulation occurs downstream of PAL transcription, indicating a block at the metabolic level invisible to transcriptomics alone. By 5 days post-infection, cytokinin accumulation coincides with nodulin gene induction and phospholipid remodeling consistent with activation of the legume symbiosis program during syncytium maturation. Together, these findings establish that compatibility arises not from failed recognition but from progressive immune dismantling, including suppression of defense chemistry and co-option of the legume-rhizobium symbiosis machinery.

Soybean cyst nematode (SCN, Heterodera glycines) causes major yield losses, and Rhg1 locus-mediated genetic resistance is becoming less effective. Hormonal signaling pathways, particularly salicylic acid (SA) and gibberellic acid (GA), are increasingly implicated in nematode resistance, but their use in plant protection remains underexplored. Here, we tested exogenous application of chemical modulators of these pathways for effects on SCN resistance and dependence on the presence or absence of Rhg1-b. We found that foliar application of the SA mimic acibenzolar-S-methyl (ASM) or the systemic acquired resistance mediator pipecolic acid (Pip) conferred strong, genotype-independent resistance, comparable to genetic resistance at Rhg1. Combining ASM with the GA biosynthesis inhibitor paclobutrazol (PBZ) synergistically enhanced protection, reducing cyst formation by 39.2% and effectively making plants moderately resistant to SCN. These effects were observed in the susceptible cultivar Williams 82, as well as across near-isogenic lines with varying Rhg1 copy numbers. ASM alone boosted resistance in resistant Rhg1-b and susceptible Rhg1-c backgrounds, whereas PBZ provided additional benefits only in Rhg1-c, revealing genotype-specific interactions between hormonal signaling and host resistance. Targeted modulation of SA and GA pathways thus provides an effective and sustainable strategy to suppress SCN, complementing and extending the durability of genetic resistance. [ ] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Detecting genomic regions under selection is essential for understanding how populations adapt to different environments, yet it remains challenging due to

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops¹, like that of the grain and bioenergy crop sorghum^2,3,4,5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets⁶. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

Soybean [Glycine max (L.) Merr.] is a critical crop globally, valued for its protein and oil content. However, historical bottlenecks have constrained genetic diversity in soybean, particularly in high-latitude regions such as North Dakota, where environmental conditions necessitate maturity group (MG) 00 and 0 cultivars. This genetic diversity study examines the North Dakota State University (NDSU) soybean breeding program using pedigree, coefficient of parentage (CP), and SNP-based analyses. Pedigree tracing of 40 NDSU cultivars revealed a genetic base derived from 49 founders. CP analysis confirmed these findings, emphasizing dependence on limited germplasm, with the top ten founders accounting for over 70% of the genetic background and Mandarin (Ottawa) alone contributing 24%. SNP-based dendrograms and genetic relationship structures demonstrate the relationships among cultivars and founders. Notably, the specialty food grade natto cultivars formed a distinct cluster unrelated to commodity soybean. Population structure analyses emphasized the reliance on specific ancestral germplasm for breeding. This study underscores the need to diversify breeding materials to prevent genetic gain plateaus in MG 00 and 0 soybeans, thereby enhancing yield potential and adaptability in high-latitude regions.

Background: The soybean cyst nematode (SCN) is a persistent threat to soybean production. SCN populations continually overcome resistant cultivars, causing significant yield losses. Studies conducted with a single reference genome restrict our understanding of intraspecific diversity, masking significant mechanisms of virulence evolution and host adaptation. Here we report a pangenome constructed of nine SCN populations of different pathotypes, including eight newly generated high-fidelity genome assemblies. Results: We detected over 19,000 orthologous gene families and more than 12,000 putative secreted proteins in SCN. Combined, these data indicate substantial diversity across populations. Gene content analysis showed that 35% of gene families were the conserved core, 15% were soft-core, and 48% were accessory. Evidence of rapid evolution was identified in a high portion (40%) of core single-copy genes, most notably inside the protein domains responsible for host recognition and immune modulation. Analysis of gene-family expansion revealed extensive duplication and loss across lineages, suggesting ongoing paralog turnover within SCN populations. Finally, a graph-based pangenome enabled the identification of numerous structural variants within regions under selection. Conclusions: Our study highlights substantial genetic variation in SCN that is not captured by single-reference analyses. By integrating multiple high-quality assemblies, we show that the SCN genome is highly dynamic, with extensive gene duplication and loss as well as structural variation shaping the differences among nematode populations. Collectively, the SCN pangenome provides a robust resource for studying virulence and adaptation mechanisms in SCN and establishes a genomic foundation for the development of more precise management strategies.

Stingless bees serve as crucial pollinators and are increasingly recognized as models for investigating behavioral and genomic evolution in insects. In the

The soybean cyst nematode (SCN), Heterodera glycines, remains the most damaging pathogen of soybean worldwide. Genomic advances over the past two decades have transformed our understanding of both the nematode and its host. On the soybean side, genome sequencing, pangenome development, and multi-omics studies have clarified how classical resistance loci such as Rhg1 and Rhg4 function while also revealing a broader and more complex landscape of resistance mechanisms. On the nematode side, effector discovery, high-quality genome assemblies, and evolutionary analyses have shed light on how SCN adapts to resistant cultivars and remodels host cellular processes. Despite these advances, overreliance on a single resistance source, PI 88788, continues to accelerate virulence shifts in SCN populations. This underscores the urgent need for diversified resistance, improved monitoring of nematode adaptation, and deeper mechanistic insight into the interaction. In this review, we integrate current knowledge of soybean–SCN interactions across genomics, transcriptomics, proteomics, cell biology, and microbiome research. We highlight how integrative functional genomics is reshaping the discovery of resistance genes, clarifying nematode virulence strategies, and guiding the development of more durable management approaches. Finally, we outline emerging directions, including pangenomics, dual host–pathogen analyses, and predictive breeding, that are expected to advance innovation in SCN control. [ ] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum, and many other crops that were not homogenized during the green revolution, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.