Category: Pub Med

Proc Natl Acad Sci U S A. 2026 Aug 25;123(34):e2610136123. doi: 10.1073/pnas.2610136123. Epub 2026 Aug 18.

ABSTRACT

Extensive selection for yield and disease resistance during tomato crop improvement has led to flavor loss in modern commercial tomatoes in comparison with heirloom varieties. To investigate the chemical and genetic architecture of tomato flavor through both domestication and improvement, we analyzed flavor-related chemicals across 558 globally collected accessions comprising wild relatives, semidomesticated and domesticated populations, including uncharacterized Latin American accessions. Key flavor volatiles exhibit major differences across accessions. A genome-wide association study was used to detect associations between genetic loci and flavor-related chemical contents, including sugars, acids, and volatiles. Multiple genetic loci linked to known genes encoding flavor metabolism enzymes, as well as many new loci, were identified. Among the newly identified loci, a gene encoding a previously uncharacterized lipase (Sl-LIP100) was experimentally proven to have an important role in synthesis of lipid-derived flavor volatiles. This enzyme is responsible for synthesis of several important five- and six-carbon flavor volatiles. In sum, this study provides chemical and genetic insights into the evolution of tomato flavor during domestication and subsequent improvement, identifying the complexity of genetic control of fruit flavor chemicals as well as a number of new alleles that can be used to improve the contents of flavor-linked chemicals.

PMID:42611996 | DOI:10.1073/pnas.2610136123

Front Plant Sci. 2026 Jul 23;17:1870120. doi: 10.3389/fpls.2026.1870120. eCollection 2026.

ABSTRACT

Tall fescue (Festuca arundinacea Schreb.) is a cool-season, allohexaploid perennial grass used for forage, soil conservation, and turf. In the United States, it is mainly adapted to the transition zone between the temperate North and mild South, with broad distribution in central and eastern regions. Forage yield depends on genotype, fertilization, and environmental conditions. As the performance of genotypes for tall fescue biomass yield is significantly affected by genotype-by-environment interaction (G×E), we evaluated biomass yield and its stability for 14 tall fescue genotypes across eight location-year combinations in the United States and Canada using 434 observations from a multi-environment trial. We analyzed data using additive main effects and multiplicative interaction (AMMI), genotype plus G×E (GGE) biplot, and restricted maximum likelihood (REML)-based mixed models to estimate best linear unbiased predictions (BLUPs). AMMI analysis revealed significant genotype, environment, and G×E effects (P < 0.001), with the first two interaction principal component axes together explaining a total of 81.8% of the interaction variance. The GGE biplot corroborated environment-specific genotype performance, supported mega-environment delineation, and identified winning genotypes (g2t and k21) within environmental clusters. Mean vs. stability and ideal genotype analyses indicated that k21 and jmx were among the most favorable genotypes for combined yield performance and stability across environments. Mixed-model BLUP estimates and probability-based ranking further supported these findings under partially unbalanced data. For simultaneous selection for productivity and stability, a Yield Weighted Stability Index (YWSI) was calculated by integrating BLUP-predicted yield with AMMI-based stability, providing a composite criterion for comparative evaluation of genotype performance. The YWSI results were consistent with those obtained from the other analytical approaches. The combined use of AMMI, GGE, BLUP, and YWSI provided a comprehensive framework for characterizing G×E patterns and facilitating genotype evaluation across diverse environments.

PMID:42564454 | PMC:PMC13442827 | DOI:10.3389/fpls.2026.1870120

Am J Bot. 2026 Aug 7:e70246. doi: 10.1002/ajb2.70246. Online ahead of print.

ABSTRACT

PREMISE: Root hemiparasites form haustoria in belowground roots of hosts to extract nutrients and water from the surrounding hosts. Through parasitic symbiosis, these plants disproportionately affect plant communities relative to their abundance by reducing host size, altering nutrient flow, and eventually increasing local biodiversity. Their prevalence and potential as keystone species position hemiparasites as important drivers of community structure.

METHODS: In a 2-year study at the Rocky Mountain Biological Laboratory, we selected paired presence and absence plots for three species of hemiparasitic Castilleja across seven study sites to explore the association of Castilleja with differences in the structure of montane plant communities. Our objectives were to (1) observe the relationship between three hemiparasitic Castilleja species and plant community diversity and composition and (2) assess the host range and preference for each species in situ using direct and indirect sampling. Percentage cover of all species was recorded to assess the effect of Castilleja presence on plant community diversity and composition. To assess host range and preference and to support nearest-neighbor and indicator-species analyses, we excavated Castilleja individuals to observe haustorial connections.

RESULTS: Across sites, species, and years, the presence of Castilleja was consistently correlated with increased plant biodiversity and site-specific differences in community composition. Excavations suggested that Castilleja species are generalist hemiparasites with some preference for common, dominant hosts.

CONCLUSIONS: Our results identify a positive relationship between Castilleja presence and local plant community diversity and support the interpretation that these species act as generalist hemiparasites.

PMID:42563626 | DOI:10.1002/ajb2.70246

Int Microbiol. 2026 Aug 6. doi: 10.1007/s10123-026-00875-4. Online ahead of print.

ABSTRACT

Bacterial communities play important roles in the plant phyllosphere. Both microbial communities and their hosts exhibit endogenous circadian rhythms while simultaneously responding to environmental changes across the diurnal cycle. However, the interaction between the host and microbiome is still poorly understood. Here, we exploit paired sequencing data of host transcriptome and microbiome derived from diverse maize genotypes in field conditions and under two contrasting diurnal periods. Expression patterns of known maize circadian clock genes were consistent with the expected sampling phases. Groups of co-expressed genes that responded to diurnal periods were associated with nucleic acid-binding, heat stress responses, and photosynthesis. Microbiome analysis revealed only modest differences in alpha diversity between midday and midnight samples. However, beta diversity indicated a significant shift in community composition. Co-occurrence network analysis identified keystone taxa specific to each time point, suggesting time-dependent ecological roles within the phyllosphere microbiome. Cross-correlation analyses between host gene expression and bacterial taxon abundance revealed a greater number of host-microbe associations during the night. Several canonical circadian clock genes significantly correlated with microbial taxa. Our findings provide initial evidence for diurnal associations between host gene expression and leaf-associated bacteriome, suggesting that maize diurnal transcriptional dynamics, including the activity of circadian clock genes, may contribute to shaping the composition and functional potential of the phyllosphere microbiome.

PMID:42557505 | DOI:10.1007/s10123-026-00875-4

Microbiol Mol Biol Rev. 2026 Aug 5:e0001226. doi: 10.1128/mmbr.00012-26. Online ahead of print.

ABSTRACT

SUMMARYLiquid-liquid phase separation (LLPS) drives the formation of biomolecular condensates, a conserved phenomenon across eukaryotes. This process governs diverse cellular programs, from stress response and morphogenesis to disease pathology. Over the past two decades, the regulatory impact of biomolecular condensates in fungal biology has become increasingly recognized. In this review, we examine the fundamental molecular mechanisms driving LLPS, evaluate the current evidence for LLPS in macromolecular organization and cellular regulation in fungi, and outline the tools employed to study this phenomenon. Lastly, we highlight the challenges of bridging the gap between the in vitro behavior of biomolecular condensates and their complex regulatory functions in vivo within fungal biology.

PMID:42554499 | DOI:10.1128/mmbr.00012-26

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