Category: Pub Med

G3 (Bethesda). 2026 Aug 5:jkag196. doi: 10.1093/g3journal/jkag196. Online ahead of print.

ABSTRACT

Accurate genotyping accelerates crop improvement, yet long-read sequencing remains underused in breeding due to cost. We present a scalable long-read low-pass (LRLP) sequencing framework for high-throughput variant discovery and trait mapping. Using PacBio HiFi reads in an allotetraploid peanut (Arachis hypogaea; AABB, 2n = 4x = 40) MAGIC population, we generated both LRLP and short-read low-pass (SRLP) data. At comparable depths, LRLP achieved substantially greater whole-genome and gene-space coverage than SRLP. Data were analyzed using both a single-reference genome and an 18-parent pangenome graph constructed with KhufuPan, a new tool for graph-based genotyping. Across analytical approaches, LRLP consistently identified more SNPs, indels (2-1,000 bp), and structural variants (>1 kb) than SRLP, improving genotype resolution and selection accuracy, particularly for large structural variants. By reducing cost barriers and increasing variant discovery in complex genomes, LRLP provides a practical path for deploying advanced genomics in under-resourced and orphan crops critical to global food security.

PMID:42552613 | DOI:10.1093/g3journal/jkag196

Plant Cell. 2026 Aug 2:koag232. doi: 10.1093/plcell/koag232. Online ahead of print.

ABSTRACT

Soybean cyst nematodes parasitize soybean roots by inducing the formation of multinucleate syncytia to feed and complete their life cycle. However, the molecular basis of syncytia initiation and development remains limited. Here, we generated an integrated single-nucleus RNA and chromatin accessibility profile of soybean roots from infected and uninfected plants. We profiled 56,448 high-quality nuclei and identified all major root cell types, including distinct subpopulations likely enriched with syncytial nuclei. Transcriptomic and chromatin accessibility analyses support their procambium cell signature that progresses through distinct stages associated with immune suppression, cell fusion, and endoreduplication. Integrative gene expression and transcription factor motif chromatin accessibility analyses predicted CAMTA1, as a potential transcriptional repressor of defense-related genes including receptor-like kinases, whereas MYB, MYB-related, and E2F likely act as potential transcriptional activators that coordinate cell wall remodeling, chromatin modification and DNA replication, respectively, across developmental trajectories. These findings provide areas to pursue in the future to understand mechanistic insights into host reprogramming during nematode parasitism and serve as a foundational resource for engineering nematode-resistant soybean.

PMID:42542330 | DOI:10.1093/plcell/koag232

New Phytol. 2026 Jul 29. doi: 10.1111/nph.71478. Online ahead of print.

ABSTRACT

Methyl salicylate (MeSA) plays diverse roles in the aerial parts of plants. By contrast, its biosynthesis and function in roots remain poorly understood. Here, we investigated root MeSA biosynthesis and function in tomato. Genome-wide association studies (GWAS) were performed using root MeSA levels as the phenotype in a diversity panel of 167 accessions to identify associated loci. Candidate genes were biochemically characterized, and the role of MeSA in defense against root-knot nematode (RKN, Meloidogyne incognita) was evaluated using transgenic plants. MeSA was identified as a major root volatile in tomato and showed a domestication-associated reduction. GWAS revealed multiple loci associated with natural variation in root MeSA, including a major locus on Chromosome 9 encoding the salicylic acid methyltransferase (SlSAMT). SlSAMT-overexpressing plants showed reduced resistance to RKNs, whereas SlSAMT-knockdown plants exhibited enhanced resistance. Our results suggest complex roles of MeSA and the salicylic acid (SA) signaling pathway in belowground plant defense. The SA signaling pathway likely plays critical roles in protecting roots against diverse natural enemies, including RKNs. Nevertheless, RKNs appear to have co-opted MeSA as a host-location signal, and the domestication-associated reduction of root MeSA in tomato has likely contributed to enhanced resistance against RKNs.

PMID:42528076 | DOI:10.1111/nph.71478

Front Plant Sci. 2026 Jul 13;17:1854406. doi: 10.3389/fpls.2026.1854406. eCollection 2026.

ABSTRACT

Plant-driven lighting control has been proposed as a strategy to regulate supplemental light-emitting diode (LED) intensity according to real-time plant physiological status. This study developed a multiple linear regression (MLR) model to predict quantum yield of photosystem II (Φ_PSII) from environmental variables and evaluated its integration into a chlorophyll fluorescence-based biofeedback light control. The model incorporated light intensity, CO₂ concentration, air temperature, vapor pressure deficit, short-term light history, and diurnal effects. In a greenhouse validation experiment, supplemental lighting was regulated using either direct chlorophyll fluorometer measurements of Φ_PSII (sensor-based control) or Φ_PSII values predicted by the machine learning model (ML-based control), and compared with a constant photosynthetic photon flux density (PPFD) treatment. Both sensor- and ML-based control stabilized photochemical activity across the photoperiod relative to constant PPFD. Although plant growth did not differ among treatments, sensor-based ETR control achieved the highest energy use efficiency for LED lighting in this study. These findings demonstrate the feasibility of integrating predictive ML models into plant-based lighting control systems and indicate that sensor-based biofeedback control improved the energy-use efficiency of greenhouse supplemental lighting without compromising crop growth.

PMID:42516599 | PMC:PMC13402182 | DOI:10.3389/fpls.2026.1854406

Plant Genome. 2026 Sep;19(3):e70282. doi: 10.1002/tpg2.70282.

ABSTRACT

Zoysiagrass (Zoysia spp.) is an important warm-season turfgrass cultivated across tropical, subtropical, and temperate regions of the world. The genus is characterized by the presence of salt-secreting glands on the adaxial leaf surface, which contribute to its high salt tolerance. In this study, we analyzed an interspecific F₂ population, derived from selfing an F₁ from a cross between Z. japonica acc. Meyer and Z. matrella acc. PI 231146, for variation in adaxial salt gland density, leaf width, and vein count. Using composite interval mapping with a previously constructed genetic map as a framework, we identified three quantitative trait loci (QTL) for leaf width, two QTL for vein count, and two QTL for salt gland density. We complemented the QTL analysis with bulked segregant RNA-seq (BSR-seq) to identify shared genomic regions and candidate genes for leaf width and salt gland density. BSR-seq identified four trait-associated regions, but only a single region identified for leaf width on Chr08 overlapped with a QTL for the same trait. We highlight putative candidate genes underlying the leaf width and salt gland density QTL and discuss their potential roles in leaf development. Together, the QTL and candidate genes provide an important resource for breeding stress-resilient Zoysia germplasm.

PMID:42495887 | DOI:10.1002/tpg2.70282

Plant Dis. 2026 Jul 16:PDIS09251939RE. doi: 10.1094/PDIS-09-25-1939-RE. Online ahead of print.

ABSTRACT

The soybean cyst nematode (SCN), Heterodera glycines, is a significant yield-limiting threat to soybean production in the United States. Although growing resistant soybean cultivars is the most effective management strategy, prolonged use of PI 88788-derived-resistant cultivars has led to a decrease in effectiveness of this mode of genetic resistance (the rhg1-b allele). The hypothesis we tested was whether soybean cultivars with resistance genes/quantitative trait loci (QTL) combinations other than rhg1-b could suppress population densities and prevent or delay virulence shifts. In four independent field experiments, the effects of soybean genotypes with different SCN resistance gene combinations, grown continuously and in annual rotations, on SCN egg population densities and virulence profiles were investigated. Field experiments were established in Illinois, Missouri, and Central and Northern Iowa in 2019 and conducted for four successive growing seasons. We utilized different combinations of resistance genes and QTL, including rhg1-a/rhg1-b, rhg2, Rhg4, GmSNAP02-ins, GmSNAP14-ins, cqSCN-006, cqSCN-007, and cqSCN10. Microplots inclusive of 12 treatments with three replications were infested with SCN populations with known virulence profiles. Our results showed that the population density and Heterodera glycines (HG) types were influenced primarily by the rotation schemes and the virulence profile of SCN inoculum used. Continuous use of any single genotype increased virulence on resistance sources that shared common resistance genes, whereas deploying resistance genes in rotation slowed the increase in nematode virulence and reduced overall population densities. However, some rotation schemes accelerated the development of virulence on ‘Peking’ and PI 90763. Our results suggest that resistance genes should be deployed strategically in rotation schemes for more durable SCN management.

PMID:42461806 | DOI:10.1094/PDIS-09-25-1939-RE

Int J Mol Sci. 2026 Jun 26;27(13):5760. doi: 10.3390/ijms27135760.

ABSTRACT

Seashore paspalum (Paspalum vaginatum), a salinity-tolerant turfgrass, lacks well-characterized viral profiles. This study reports the discovery of a novel virus, tentatively named Paspalum latent virus (PaLV), representing a new taxon within the Alphaflexiviridae. Using high-throughput sequencing and RACE PCR, the 6995 nt genome was determined, revealing five open reading frames. Notably, PaLV lacks the AlkB domain and exhibits unique features, including overlapping start-stop codons (ORF4/ORF5) and a second in-frame AUG in the coat protein (CP) region. Phylogenetic analysis of the replicase placed PaLV in a distinct clade, separate from Potexvirus and Lolavirus. Despite low sequence identity, AlphaFold2 revealed conserved CP structural domains. Genetic analysis of 11 isolates showed low diversity and strong purifying selection. Pathogenicity assays through mechanical transmission demonstrated a broad but latent host range, including Zea mays and Sorghum spp. These findings suggest PaLV represents a novel species within a putatively new genus, Paspalovirus. Given its 90% incidence rate and latent profile, the RT-PCR assay developed here is vital for routine molecular diagnostics in turfgrass management and germplasm conservation.

PMID:42450033 | DOI:10.3390/ijms27135760

Microbiol Resour Announc. 2026 Jul 10:e0033426. doi: 10.1128/mra.00334-26. Online ahead of print.

ABSTRACT

We sequenced the genomes of 77 bacterial strains, tentatively identified as Enterobacter. Of these, 71 were identified as Enterobacter based on genomic analysis. These strains span 11 species of diverse ecological and geographical origin.

PMID:42429961 | DOI:10.1128/mra.00334-26

Nat Commun. 2026 Jul 9. doi: 10.1038/s41467-026-75205-3. Online ahead of print.

ABSTRACT

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.

PMID:42426026 | DOI:10.1038/s41467-026-75205-3

G3 (Bethesda). 2026 Jul 8:jkag175. doi: 10.1093/g3journal/jkag175. Online ahead of print.

ABSTRACT

The Runner-type peanut (Arachis hypogaea L.) cultivar ‘Tifguard’ carries an introgressed chromosomal segment on chromosome A09 from A. cardenasii that confers resistance to root-knot nematode (RKN). Despite this, a proportion of ‘Tifguard’ plants show RKN symptoms, which could plausibly be attributed to seed mixture or outcrossing. However, recent work has shown that cultivated peanut exhibits surprisingly frequent large-scale chromosomal instability (1-5%), raising the possibility that resistance loss could arise from spontaneous structural genomic change. To test these possibilities, we grew foundation seed in an RKN-infested field and collected symptomatic and asymptomatic plants. Lineages derived by single-seed descent were genotyped using the Axiom Arachis 48K SNP array v2 and whole-genome sequencing. Symptomatic lineages lacked the A. cardenasii introgression on chromosome A09 and instead carried the complete endogenous A. hypogaea A09 region at the expected dosage. There was no evidence of large-scale homoeologous exchange, deletion, or other genomic instability affecting this chromosome. Most susceptible plants were closely related to resistant ‘Tifguard’ but lacked the A09 introgression, with a smaller proportion assignable to known nematode-susceptible cultivars, implicating seed mixture with a possible contribution from cross-pollination rather than genomic instability. Because resistance depends on a single major-effect segment, rare events have disproportionate phenotypic impact, placing high demands on genetic purity. For important traits conferred by major loci, marker-based testing across seed-increase stages could verify trait retention directly, and is increasingly practical as marker costs decline.

PMID:42417136 | DOI:10.1093/g3journal/jkag175