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PubMed2026

Quantitative trait locus qLDC5 regulates primary root branching in an auxin-dependent manner.

L-type lateral root (LLR) density determines root system architecture, affecting nutrient acquisition in rice (Oryza sativa L.), particularly under low-phosphorus conditions. Previous studies identified genotypic differences in LLR density and a quantitative trait locus (QTL) enhancing LLR density on crown roots (qLDC5). We showed that LLR densities on crown and primary roots were closely correlated and confirmed higher LLR density on primary roots in qLDC5 donor DJ123 compared with the African variety NERICA4 using X-ray micro-computed tomography. We confirmed the qLDC5 effect in a field experiment for LLR density on primary roots. LLR densities on primary and crown roots, therefore, appear under similar genetic control. Developmental analyses revealed that DJ123 and NDJ188-a derivative line harboring qLDC5-initiate more lateral root primordia than NERICA4, with a higher proportion progressing to elongation, but that exogenous auxin application reversed this ranking. Within qLDC5, auxin biosynthesis gene OsYUCCA2 and auxin response factor OsARF15 were up-regulated in DJ123. Transcriptome analysis revealed an indirect auxin-mediated regulatory network underlying LLR variation. Differentially expressed genes in DJ123 and NDJ188 were enriched for ent-kaurene and gibberellin metabolism, including the robust induction of OsGA2ox5. These findings suggest qLDC5 increases lateral root density by coordinating gibberellin, auxin, and terpene pathways.

Oryza↗
PubMed2026

The potential of considering photosynthesis parameters in crop yield breeding by genomic prediction.

To meet the growing demand for agricultural products, optimizing photosynthesis is a promising strategy to improve crop yields. Phenotypic variance in photosynthesis has been observed within or between species. To explore the potential of integrating photosynthetic parameters into crop breeding programs, we explored the genetic variation in photosynthesis by assessing photosynthesis-related parameters across plant development in 631 barley recombinant inbred lines (RILs) from eight HvDRR subpopulations under field conditions. The genetic complexity of these parameters was resolved by analyses of bi-parental and multi-parental quantitative trait loci (QTLs). Finally, we examined the merit of integrating photosynthesis-related parameters in genomic prediction of yield and its components. Significant genotypic variations of the photosynthesis-related parameters were found among the RILs, with their heritability ranging from 0.38 to 0.54. The multiple QTLs and dynamic QTLs for photosynthesis observed across different developmental stages underlined the complexity of the genetics of photosynthesis in barley. The considerably higher percentage of phenotypic variance explained for genomic prediction than multi-parental QTL analysis illustrates that the photosynthesis-related parameters are inherited in a more complex way than classical agronomic traits. Notably, the prediction ability for yield was increased by integrating the photosynthesis-related parameters of some developmental stages into genomic prediction models. Thus, our results suggest a novel perspective on increasing the efficiency of crop breeding programs by integrating photosynthesis-related parameters into prediction models.

Photosynthesis↗
PubMed2026

The link between phosphate starvation-triggered anthocyanin biosynthesis and jasmonate-driven regulation in tomato.

Phosphate Starvation Response (PSR) in plants integrates inorganic phosphate (Pi) sensing with hormonal and metabolic reprogramming. Recent evidence supports a PSR-jasmonate (JA)-anthocyanin axis in which the PSR-associated PHOSPHATE STARVATION RESPONSE (PHR)/PHR-like-SYG1-PHO81-XPR1-inositol pyrophosphate 8 (PHR/PHL-SPX-InsP8) module gates transcriptional activation, while the core JA components JASMONATE ZIM-DOMAIN (JAZ) and MYELOCYTOMATOSIS 2 (MYC2) mediate hormone-induced activation of secondary metabolism. In Solanum lycopersicum, PHR/PHL transcription factors (TFs) serve as core PSR hubs, with expanded regulatory networks and InsP-associated control layers that tune SPX buffering and transcriptional output. Downstream, JA signaling and MYC2-dependent transcription interface with anthocyanin regulators, including key MYB and bHLH TFs that form the MYB-basic helix-loop-helix (bHLH)-WD40 repeat (MBW) complex, thereby regulating tissue capacity for pigmentation under Pi starvation (PiS). Anthocyanin-rich tomato cultivars such as 'Indigo Rose' exemplify how genetic configuration can enhance MBW responsiveness and potentiate pigment accumulation under PiS. Here, we collate recent advances linking PSR gating, JA response, and anthocyanin biosynthesis regulation in tomato, and propose a working model with testable predictions to accelerate causal validation, and enable breeding strategies targeting phosphorus use efficiency and nutritional quality.

Solanum lycopersicum↗
PubMed2026

An efficient woody plant protoplast platform enables transgene-free multiplex genome editing and rapid trait validation in pear.

Multiplex editing is crucial for analysing complex multiple-gene traits in woody plants, yet its application remains limited because of low transformation efficiency and lengthy regeneration cycles. To overcome these barriers, in this study we establish an efficient protoplast isolation protocol for pear (Pyrus) that employs 1.0% cellulase R10 and 0.4% macerozyme R10 with an 8.5 h digestion. Its broad applicability using different digestion times across seven other economically important woody plants is demonstrated. Coupling a 40% PEG-4000-mediated transfection regimen with DNA-free CRISPR/Cas9 ribonucleoprotein (RNP) delivery enables multiplex genome editing in isolated protoplasts. Using this platform, we simultaneously disrupted the key components of the chloroplast division apparatus ARC3, PARC6, and FtsZ2-1a in Pyrus bretschneideri and found that it consistently reproduced macro-chloroplast abnormalities, confirming effective multigene perturbation within a single cellular context. Notably, failure of chloroplast division activated chloroplast-to-nucleus retrograde signaling, as evidenced by the induction of the nuclear stress-response genes RBOHD and ZAT12, a concomitant surge in reactive oxygen species, and progression to severe cellular deformation. Thus, our study establishes a rapid, cross-genus protoplast-RNP workflow that enables DNA-free multiplex editing and accelerates genotype-to-phenotype analyses in woody perennials. The approach provides a practical foundation for functional genomics and supports advances in non-transgenic precision breeding of tree crops.

Protoplasts↗
PubMed2026

Expanding the scope of precision editing in seaweeds through the application of a novel CRISPR-associated nuclease 12a-aligned CRISPR system in Ulva prolifera.

Seaweeds, such as the fast-growing green alga Ulva prolifera, can be harnessed as valuable marine crops. The lack of scalable genome-editing tools hampers functional genomics to explore and elucidate algal molecular pathways with industrial importance. Here, we expanded precision genome modification in seaweeds by successfully demonstrating gene editing with a transgene-free AT-rich-targeting CRISPR-associated protein (Cas) system in U. prolifera. By evaluating various delivery buffers, comparing different Cas systems, and optimizing incubation temperatures, we determined suitable conditions for more widespread applicability of a novel Cas12a-aligned ST8 editor. We obtained >50 ST8-mediated knockout mutants of a toxin-based endogenous marker gene, UpAPT, at 28 °C post-delivery incubations. Our work diversified the applicable genome-editing tools in seaweeds, advancing algal functional genomics and providing more strategies to precisely target unexplored seaweed resources.

Ulva↗
PubMed2026

Beyond the CO-FT regulatory module: E1 and PHYA emerge as players in photoperiodic regulation of flowering in legumes.

The legume family (Fabaceae) is the third largest in plants and includes several crop species that are able to fix nitrogen, promote soil health, and contribute to food security worldwide. Recent progress in legume genetics and genomics allowed the identification of photoperiod-dependent flowering loci, which were incorporated into specific signalling networks. Functional characterization of these regulators revealed new roles for known photoreceptors such as phytochrome A, and it also identified legume-specific B3 domain transcriptional factors (E1 and E1-like proteins). This suggests some diversification from the traditional CONSTANS-FLOWERING LOCUS T module present in other angiosperms. Although most of the findings discussed herein pertain to species from the two main legume clades, the Galegoids (e.g. alfalfa, clover, and pea) and the Phaseoloids (e.g. common bean, soybean, cowpea, and pigeon pea), research on flowering regulation in the basal Genistoid clade (e.g. lupins) will also be addressed. We propose that functional diversification of photoperiod-dependent flowering strategies in the different legume species could have contributed to their environmental adaptation and allowed their geographical expansion and success worldwide.

Photoperiod↗
PubMed2026

OsICL-associated metabolic reprogramming during dehydration in rice is regulated by ABA and modulated by ACC and its metabolites.

Drought coordinates hormonal, transcriptional, and metabolic reprogramming, but how abscisic acid (ABA) and 1-aminocyclopropane-1-carboxylic acid (ACC) jointly shape cereal dehydration responses remains unclear. We integrated hormone profiling, transcriptome and promoter analyses, synthetic promoter assays, and metabolite profiling in rice. ABA and ACC contents increased markedly in rice shoots under moderate soil water deficit. Combined ABA + ACC treatment showed larger absolute overlaps with dehydration-responsive genes than either ABA or ACC treatment alone in shoots; in roots, this pattern was observed for induced but not repressed genes. Promoters of dehydration- and ABA-inducible genes were enriched in ACGT-core motifs, including a CGTACG core preferentially embedded in ACGTACGT, designated the eXtended ACGT box (Xbox). Multimerised Xbox conferred transcriptional induction under soil water deficit and in response to ABA. OsICL was induced under soil water deficit and by ABA or ACC; in shoots, combined ABA + ACC treatment produced the highest mean transcript accumulation. OsICL overexpression and knockout lines showed altered organic-acid, sugar, and amino-acid profiles, particularly under soil water deficit, but several metabolites changed in the same direction in both line classes. These findings support an ABA-centred, ACC-modulated model of dehydration-responsive transcription and associate OsICL regulation with broader, condition-dependent changes in primary metabolism.

Oryza sativa↗
PubMed2026

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.

The rhesus macaque (Macaca mulatta) is one of the most widely used animal models in biomedical research, both as it resembles humans in key biological aspects and as it is characterized by a broad geographic range. Most of the individuals housed in U.S. research colonies have been sampled from either China or India, though notably the source population of these animals has significantly shifted over time. Given the substantial genetic and immunological differences between these populations, a deeper understanding of the underlying population structure is critically important for biomedical interpretation. Despite this, the demographic histories of these two populations remain poorly resolved. Here, we present an analysis of whole-genome, PacBio HiFi long-read sequencing data from ten unrelated individuals of each population, applying four related model- and non-model based demographic inference approaches, in order to reconstruct their ancestral history. We evaluated the fit of the subsequently estimated models against the empirical data, and incorporated underlying uncertainty in the mutation rates used for scaling. We inferred a well-fitting population history characterized by substantial structure between Chinese and Indian populations, with a split time ∼140,000 generations ago from an ancestral population of ∼65,000 individuals. We additionally inferred the subsequent history of size change within, and gene flow between, these populations, reaching the current estimated sizes of ∼220,000 individuals in the Chinese population and ∼14,000 individuals in the Indian population. The robust baseline demographic model established in this study will serve as a valuable resource for future research on this species, including for improved fine-scale recombination mapping, selection inference, and association studies.

Cercopithecidae↗
PubMed2026

High-grade astrocytoma with piloid features: a clinical and genomic analysis of prognostic factors using a large cohort.

BACKGROUND: High-grade astrocytoma with piloid features (HGAP) is a recently defined tumor type that is not well-understood. Prognostic factors of clinical outcomes are not well-established. METHODS: Methylation profiling was performed on tumor samples, many at the National Cancer Institute (NCI) Laboratory of Pathology, and others from publicly available sources. Methylation classifier scores of ≥ 0.90 to the HGAP class on the NCI-Bethesda classifier version 3 were included. Clinical features were collected from the medical record. Survival analyses were performed using the Kaplan-Meier and Cox-proportional hazards methods. RESULTS: The cohort comprised 421 patients. There were high rates of ATRX alteration (62%), CDKN2A/B homozygous loss (78%) and MGMT promoter methylation (53%). MAPK alterations were identified in 74% of evaluable samples. The median age was 46 years, and posterior fossa location was predominant (52%). The median overall survival (OS) was 88 months. Older age (p = 0.01) and the presence of an ATRX alteration (p = 0.04) were found to be negative prognostic factors. The presence of cystic features on magnetic resonance imaging (MRI) was found to be favorably prognostic (p = 0.01). Factors that were not significantly associated with prognosis included histologic high-grade features, CDKN2A/B homozygous deletion, MGMT promoter methylation, extent of resection, and presence of NF1 syndrome. CONCLUSIONS: This large cohort establishes relative frequencies of several important markers. Additionally, older age, the presence of an ATRX alteration, and cystic features on MRI were found to be prognostic. Our work may aid in optimizing treatment regimens for patients with this tumor type.

ATRX alteration↗
PubMed2026

Genome assembly and subgenomic interactions in Brassica napus additional lines with an alien B05 chromosome from B. juncea.

Alien chromosome addition lines hold significant value for breeding and genetic research. However, the genetic interaction between the recipient genome(s) and the alien chromosomes remain largely unclear. Here, we analyzed the genomic composition and gene expression of two purple-leaved B. napus alien addition lines carrying chromosome B05 from B. juncea: the monosomic line ZYCB3 (MAAL, 2n = 39, AACC + 1B05) and the disomic line ZY52 (DAAL, 2n = 40, AACC + 2B05). We assembled a chromosome-level genome of the DAAL ZY52 disomic line and characterized its genomic variation and chromosome introgression patterns. In addition to chromosome B05, multiple introgressed fragments derived from the donor B. juncea line ZYJC were identified, revealing extensive genome remodeling during distant hybridization and backcross breeding. We then used multi-omics approaches to explore chromosomal interactions and the regulation of anthocyanin biosynthesis. Notably, the addition of chromosome B05 was associated with stronger repression of homoeologous genes on C-subgenome chromosomes than on A-subgenome chromosomes. In ZY52, homoeologous genes on chromosome C01 showed reduced expression, whereas in the ZYCB3 monosomic line reduced expression was observed on both C01 and C02. Comparative transcriptomic and metabolomic analyses further showed that highly expressed anthocyanin biosynthesis genes (ABGs) on chromosome B05contributed to anthocyanin accumulation and the purple-leaf phenotype in both addition lines. Overall, this study provides new insights into interchromosomal interactions, genome remodeling, and phenotypic variation in alien addition lines.

Journal Article↗
PubMed2026

Potato Black Scurf and Stem Canker: Pathogen Biology, Global Distribution, and Traditional and Modern Diagnostics.

Rhizoctonia solani is a soil- and seed-borne fungal pathogen of potatoes. It is a persistent threat to potato production worldwide. The symptoms appear as black scurf on tubers and stem canker, causing severe yield and quality losses of potatoes. The pathogen reproduces asexually via hyphae and sclerotia. Its genetic diversity is organized into anastomosis groups (AGs), with AG3-PT being the predominant group on potato. The global trade of seed potatoes is very important for agricultural development; however, it has facilitated the dissemination of the pathogen across regions. Moreover, disease development is affected by environmental and agronomic factors, causing variable symptom severity and differential economic impacts. Given the pathogen's genetic complexity, accurate diagnosis is very important, necessitating a transition from traditional culture-based and biochemical methods toward molecular, genomic, and emerging digital technologies. Methods such as PCR, isothermal amplification, sequencing, sensor-based biosensing, and artificial intelligence-driven imaging have improved the detection, quantification, and noninvasive monitoring of the pathogen. Combining these diagnostic methods into a tiered framework will be helpful for precision disease surveillance, informed disease management decision-making, and the development of sustainable potato production systems.

black scurf↗
PubMed2026

Whole-genome characterization and phylogenetic placement of Fusarium oxysporum f. sp. vasinfectum isolates.

Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), remains a persistent threat to cotton production worldwide. Among the known races, Fov race 4 and its extra-virulent variants cause particularly severe losses in Upland cotton. Although several Fov genome assemblies have been assigned to races, the genomic diversity and evolutionary relationships among pathogenic and non-pathogenic isolates associated with cotton outbreaks remain poorly understood at the whole-genome level. This study addressed these gaps by generating and comparing high-quality genome assemblies of four Fusarium isolates collected from Texas cotton fields: two pathogenic (TX17-24 and TX18-9) and two non-pathogenic (TX17-6 and TX18-6). Draft assemblies were generated using Oxford Nanopore long reads and polished with Illumina reads. Comparative genomic analyses showed that pathogenic isolates possessed larger genomes and more conserved orthologous families, whereas non-pathogenic isolates contained more unique genes. Analyses of predicted secreted effectors, transposable elements, and carbohydrate-active enzymes further distinguished pathogenic and non-pathogenic lineages, suggesting roles in virulence adaptation and genome plasticity. Phylogenomic analyses using k-mer-based, assembly- and alignment-free methods incorporated all available long-read Fov genomes and revealed substantial genetic diversity within races 1 and 4, clustering isolates into multiple sublineages. These findings show that Fov race diversification is underestimated when based on traditional classification schemes and may be shaped by host specialization, geographic separation, or horizontal gene transfer. This work advances our understanding of the genomic diversity and evolutionary dynamics of Fov and establishes a foundation for improved race identification and characterization of Fusarium wilt pathogenesis in cotton.

Fusarium oxysporum↗
PubMed2026

Recent Advances in the Comprehension of Molecular and Genetic Mechanisms Underlying Yeast Biocontrol Efficacy Against Fungal Pathogens in Agriculture.

Recent advances in biotechnologies have enabled scientists to uncover biological processes across multiple research fields. Still, the molecular and genetic mechanisms underlying the biological control efficacy of yeast biocontrol agents (YBCAs) against fungal plant pathogens remain incompletely elucidated. This review focuses on recent insights into the regulatory bases and molecular interplay underlying successful disease control by YBCAs. It provides a detailed description of core antagonistic molecular mechanisms-nutrient and iron competition, mycoparasitism via cell wall degradation, antifungal compounds production, oxidative stress resistance, biofilm formation and colonization, and induction of the host defense responses-and integrates genomic, transcriptomic, proteomic, and metabolomic evidence to elucidate each mechanism. Further, how genetic engineering-based approaches that leverage omics data and functional genetics can help overcoming obstacles to translate YBCAs efficacy from laboratory conditions to the field are also discussed. Finally, the use of the CRISPR-Cas technology is recommended to better exploit how master transcription factors coordinate multiple mechanisms simultaneously; these factors are crucial for the synergistic antifungal effect, which is critical for developing highly effective YBCAs. Ultimately, the mechanism-based perspective provides a unified conceptual framework for understanding YBCAs efficacy and can guide the rational design of next-generation biocontrol agents for sustainable agriculture.

CRISPR-Cas technology↗
PubMed2026

Editorial Comment.

Explore the source record for details and available documents.

Journal Article↗
PubMed2026

Widespread Loss of Heterozygosity and Endoreduplication in Odontogenic Myxoma: Expanding the Clinicopathologic Spectrum of An Enigmatic Odontogenic Neoplasm.

Odontogenic myxoma (OM) is an uncommon, locally aggressive odontogenic neoplasm with characteristic histologic and clinico-radiographic features but with potential for histologic overlap with other odontogenic and non-odontogenic entities and a non-specific immunoprofile. Widespread loss of heterozygosity (LOH) has been recently described in rare cases of OM. The aim of this study was to determine whether widespread LOH represents a recurrent molecular signature that can be leveraged for clinical decision-making. Allele-specific copy number variation data from chromosomal microarray were generated from 7 OM, comprising a combined prospective and retrospective cohort. Four tumors arose in the mandible and 3 in the maxilla in patients ranging in age from 18 to 94 years (median: 44), with tumor size ranging from 2.2 to 13.0 cm. Variable amounts of fibrous stroma (odontogenic "fibromyxoma") were present in 4/7 OM, and hypercellularity not typically appreciated in conventional OM was present in 3/7 cases. All OM (7/7) demonstrated widespread LOH, with 5 cases showing a near-haploid/low hypodiploid genomes (multiple monosomies) and 2 cases showing evidence of pseudo-hyperdiploidy due to probable endoreduplication. Both pseudo-hyperdiploid cases were ≥10 cm in size; 1 represented local recurrence. Chromosomes 1 to 3, 6, 9, 11, 13, 15, and 22 demonstrated LOH in ≥75% of cases (chromosomes 1 to 3, 6, and 9 in 100% of cases), while chromosomes 5, 12, 19, and 20 universally retained heterozygosity. Altogether, widespread LOH is a recurrent event in OM and a novel finding in odontogenic pathology, and allele-specific copy number variation analysis can serve as a diagnostic adjunct in challenging cases.

copy number variation↗
PubMed2026

Nuclear mitochondrial sequences in great ape telomere-to-telomere genomes.

Mitochondrial sequences have integrated into the nuclear genome since the origin of eukaryotes. Recent insertions that retain homology with extant mitochondrial DNA (mtDNA), termed NUMTs, confound mtDNA sequence analysis. Here, we use great ape telomere-to-telomere (T2T) genomes to study NUMTs in bonobo, chimpanzee, human, gorilla, and Bornean and Sumatran orangutans. A phylogeny based on shared and lineage-specific NUMTs accurately recapitulates the great ape species tree topology. NUMTs are enriched at nonfunctional nonrepetitive regions of the nuclear genome and depleted within enhancers and coding sequences, suggesting negative selection. We validate the presence of a 76-kb-long heterozygous NUMT in chimpanzee, which is larger than any other NUMT observed in great apes, and find that dozens of NUMTs on the Pan Y Chromosome expanded together with palindromes. Finally, by analyzing intra-specific variation, we confirm that the vast majority of species-specific NUMTs identified in T2T assemblies are fixed or present at high frequencies in each species. Our study highlights NUMTs as a dynamic evolutionary force contributing to shaping ape genomes and is valuable for characterizing mtDNA in great apes.

Journal Article↗