- Research Article
- 10.1016/j.jgg.2025.10.007
Dual-target CRISPR-Cas12 diagnostics based on asymmetrically chemical-modified DNA probe.
- Apr 01, 2026
- Journal of genetics and genomics = Yi chuan xue bao
- Xinge Wang + 12 more +12
Publications from 2021 to 2026
Showing 10 of 91 papers
Dual-target CRISPR-Cas12 diagnostics based on asymmetrically chemical-modified DNA probe.
Engineering a Gibberellin-Switchable Dual-Use Line Based on Ent-Kaurene Oxidase Gene ZmKO1 Enables Two-Line Hybrid Seed Production in Maize.
Male-sterile systems are pivotal for maize hybrid seed production, yet existing systems are constrained by significant limitations. Here, we identified a novel single-gene-controlled recessive genic male sterility (GMS) mutant, defective in filament elongation 1 (def1), which exhibits non-elongated filaments, unopened glumes, and non-exserted anthers, yet undergoes normal microsporogenesis and produces viable pollen. Map-based cloning revealed that def1 is caused by a loss-of-function mutation in the ZmKO1 gene. Previous studies have identified ZmKO1 and ZmKO2 as the two putative KO-encoding genes in maize. Although heterologous expression evidence suggested that only ZmKO1 possesses KO activity, we demonstrate that both ZmKO1 and ZmKO2 are functional KOs for GA biosynthesis. The def1 mutant or ZmKO1 knockout lines exhibited reduced plant height during early seedling development but recovered rapidly to wild-type levels. In contrast, ZmKO2 knockout lines displayed severe dwarfism and pollen-less male sterility. These contrasting phenotypes demonstrate a clear functional divergence between the two genes. Utilising marker-assisted backcrossing and CRISPR/Cas9 editing, we generated ZmKO1-based GMS lines across diverse genetic backgrounds. These lines maintained stable male sterility and could be efficiently propagated via exogenous GA3 application under different genetic backgrounds and environments, demonstrating robust "dual-use" properties. Data indicated that this dual-use trait has no significant effect on other agronomic traits of the male sterile line and its derived hybrid combinations. Based on this, we established a novel two-line hybrid seed production system in maize, termed the Gibberellin-switchable Dual-use Line (GDL), and successfully applied it in the hybrid seed production of Chuandan 99.
Read moreTraitDiscover: An automated high-throughput platform for multimodal plant phenotyping with real-time trait analysis
Plant phenotyping is essential for elucidating genotype–environment interactions, yet conventional methods remain labor-intensive and low-throughput. TraitDiscover transcends these constraints by uniting multimodal sensing with tightly coupled hardware-software orchestration in a single, end-to-end phenotyping platform. Aligned with the ”Plant Phenotyping Trinity” framework, the system comprises a millimetre-accurate triaxial automation unit, a modular sensor array–RGB imaging, three-dimension laser scanner or LiDAR (3D), infrad (IR) thermal imaging, hyperspectral imaging (HSI), and photosynthesis (PS) imaging–and the dedicated software TraitNavigator suite into one cohesive system. A unified spatiotemporal synchronization mechanism enables robust time-series analysis and fusion of multisource phenotypic data across the entire crop growth period, while the DepthCropSeg algorithm and a night-time imaging module enhance trait extraction under complex conditions, providing G × E × P-ready, multimodal phenotypic datasets. Validation across soybean, maize, and rice trials demonstrated high sensitivity—detecting drought stress four days before visible symptoms, identifying glyphosate injury 24 hours ahead of manual scoring, and quantifying local adaption patterns across ecological gradients. While challenges remain in scaling to complex open-field conditions, TraitDiscover offers a scalable, data-driven approach to accelerate stress phenotyping and breeding decisions and is readily poised for deeper integration with AI to advance sustainable agriculture.
Read moreBiology and predatory potential of <i>Eocanthecona furcellata</i> on semi-looper, <i>Chrysodeixis eriosoma</i> in Sarangani, Mindanao Island, Philippines
Abstract. Paslon Jr FV, Parlucha JA. 2025. Biology and predatory potential of Eocanthecona furcellata on semi-looper, Chrysodeixis eriosoma in Sarangani, Mindanao Island, Philippines. Biodiversitas 26: 6197-6204. Predatory bugs play an important role in Integrated Pest Management (IPM) by naturally regulating populations of agricultural insect pests. Their use promotes sustainable agriculture by enhancing biodiversity and minimizing environmental impact. This study documents the first recorded observation of a predatory stink bug, Eocanthecona furcellata in Sarangani Province, Mindanao Island, Southern Philippines, collected from Sunn hemp (Crotalaria juncea) fields. The life cycle and predatory potential of E. furcellata were assessed under laboratory conditions using the corn semi-looper, Chrysodeixis eriosoma as prey. The freshly laid eggs of E. furcellata were initially white, gradually turning light brown, and measured 1 mm in length and 0.89 mm in width. Eggs became dark red just before hatching, with an incubation period of six days. The nymphs progressed through five instars, completing their development in an average of 15.7±0.46 days. Adult female E. furcellata were larger and lived up to 36.8±1.81 days, while male adult E. furcellata had a shorter lifespan of up to 32.3±1.34 days. Predation rates varied significantly among developmental stages, with the fifth-instar nymphs exhibiting the highest predatory efficiency, consuming an average of 23.27 second-instar C. eriosoma larvae within 48 hours. The results indicate that C. eriosoma serves as a suitable alternative prey for mass-rearing E. furcellata. Furthermore, the study highlights the potential of E. furcellata as an augmentative biological control agent for managing C. eriosoma populations in agricultural ecosystems.
Read moreNatural Variations of ZmRLR1 Mediate the Root Lodging Resistance of Maize by Regulating Root Ascorbate and Auxin Homeostasis
ABSTRACTRoot lodging is a major problem limiting crop yield and seed quality. Here, we showed that Root Lodging Resistance 1 (ZmRLR1) is specifically expressed in maize roots. The overexpression of ZmRLR1 increased the rhizosphere soil weight, stem pulling force of the internode 50 cm from the ground, total root length, and root volume. In contrast, the rhizosphere soil weight, stem pulling force of the internode 50 cm from the ground, total root length, and root volume were reduced in the Zmrlr1ems and Zmrlr1 mutants. Natural variations in the promoter of ZmRLR1 are significantly associated with the root lodging resistance of maize. ZmRLR1 positively regulates the ascorbate (AsA) content in maize roots. We further demonstrated that ZmRLR1 improved the interaction between the ZmAP2 σ subunit and ZmCHC2. The internalization of the endocytic tracer FM4‐64 is substantially reduced in the Zmrlr1ems and Zmrlr1 mutants, while auxin distribution and ZmPIN1a‐YFP localization are altered in Zmrlr1ems. The defect in the total root length of Zmrlr1ems is rescued by the exogenous application of 10 µmol L−1 AsA plus 0.01 µmol L−1 1‐naphthaleneacetic acid. Taken together, these results suggest that ZmRLR1 affects the root lodging resistance of maize by regulating root AsA and auxin homeostasis.
Read moreFirst Report of Basal Stem Rot Caused by <i>Geotrichum candidum</i> on <i>Aloe vera</i> in China
Aloe vera is a perennial evergreen herb belonging to Liliaceae Aloe, which is widely used in beauty, food, healthcare, and medicine (Kumar et al. 2019) and extensively cultivated worldwide due to its enormous commercial value. However, a stem rot disease severely restricts the development of A.vera cultivation in China (Ji et al. 2007). In 2023, the average disease incidence of A.vera Mill. with basal stem rot in Dajie Town, Daming County, Handan City, Hebei Province, was 20%. The disease initially appeared as translucent, water-soaked patches on the epidermis of basal stems. These lesions progressed from light brown to dark brown, with vascular bundles turning brown. Internal tissues softened into a soggy decay and emitted a foul odor. Nine diseased plants showing representative symptoms were collected from three greenhouses. The pathogen was isolated from diseased stems using a tissue separation method. The stem tissues were surface sterilized with 75% ethanol for 30 s, then rinsed three times with sterile distilled water, dried, transferred to potato dextrose agar (PDA) supplemented with 100 μg/ml of streptomycin sulfate, and incubated at 25℃ for 2 days. A total of six isolates with similar morphology on PDA were consistently isolated, and purified by single-spore isolation (Qiu et al. 2011). Colonies showed round, flat surfaces, white downy or powdery mycelium, clear on the reverse side. Hyphae were hyaline, septate and branched microscopically. Arthrospores were hyaline, cylindrical or oval-shaped, ranging in size from 2.5 to 7.2 μm × 0.1 to 6.2 μm (n=50). These morphological features matched those of Geotrichum candidum (Kai et al. 2021). To further confirm the identification, the internal transcribed spacer (ITS) and translation elongation factor 1 -alpha (TEF1-α) regions were amplified and sequenced from two randomly selected isolates (BAI, BAI2) using the primers ITS1/ITS4 (White et al. 1990), EF1-1018/EF1-1620R (Stielow et al. 2015). BLAST analysis revealed that the ITS sequences (PV018630, PV168341) had 100% identity to that of G. candidum and TEF1-α sequences (PV469904, PV469905) had 100% and 99% identity to that of G. candidum. A neighbor-joining phylogenetic tree based on ITS and TEF1-α indicated that BAI and BAI2 clustered with G. candidum (Saitou and Nei, 1987). BAI and BAI2 were deposited in the Life Sciences Experimental and Practical Training Center. For pathogenicity testing, healthy 1.5-year-old A.vera Mill. plants were surface disinfected with 75% ethanol, and then two 2-mm-depth wounds were punctured on each basal stem using a sterilized toothpick. Ten plants were inoculated with 10 μl of a conidial suspension (5 × 10 5 conidia per ml) obtained from 7-day-old PDA cultures and eluted with sterile distilled water (Ding et al. 2015). Ten control plants were inoculated with 10 μl of sterile distilled water. All plants were incubated at 25℃ under a 12/12-h light/dark cycle. After 10 days, all plants inoculated with BAI and BAI2 developed basal stem rot symptoms that were similar to those observed in the greenhouses. While control plants remained healthy, G. candidum was reisolated from the inoculated stems and confirmed by morphological and molecular analysis, fulfilling Koch’s postulates. Tests were repeated with consistent results. To the best of our knowledge, this is the first report of G. candidum causing basal stem rot on A. vera in China. These findings will aid the cultivation of this economically important crop by enabling early diagnosis and targeted control strategies.
Read moreDevelopment of efficient targeted insertion mediated by CRISPR-Cas12a and homology-directed repair in maize
Targeted insertion (TIN) of transgenic trait cassettes has the potential to reduce timeline and cost for GM product development and commercialization. Precise genome engineering has made remarkable progress over the last several decades, particularly with the use of site-directed nucleases as core editing machinery. However, there are still many critical factors that can impact TIN efficiency including insertion site selection, nuclease optimization and expression, donor vector design, gene delivery, and stable event regeneration. Here, we develop workflows for target site sequence identification and gRNA screening for CRISPR-Cas12a system and demonstrate its successful application for TIN in maize with donor sequences up to 10 kilobase pairs (kb) in size. We first prioritize genomic regions for inserting transgenes in silico using bioinformatics tools and then test gRNA performance using a leaf protoplast transient assay. Despite its known low efficiency, we identify homology-directed repair (HDR) as the preferential pathway for directing targeted insertions of large sequences in immature embryos and demonstrate double-junction integrations at a rate of up to 4%. We further apply a molecular analysis workflow using large amplicon TaqMan assays and nanopore sequencing for streamlined identification and characterization of high-quality insertion events with intact large inserts. Analysis of TIN events across generations suggests that efficiency bottlenecks are not limited to donor targeted integration; attrition in efficiency also results from partial or additional donor insertion, chimerism, and close linkage with undesired sequence insertions such as those encoding the editing machinery. This work represents a major step forward in realizing the potential of precise genome engineering in maize for basic research and biotech trait development applications.
Read moreA Benchmark Framework for the Fast and Reliable Evaluation of Zeolite Surface Stability
Accurately identifying the external surface structure and crystal morphology of zeolites is essential for establishing structure–performance relationships. Surface free energy serves as a quantitative descriptor of surface stability, which is a prerequisite for theoretical investigations of surface properties. However, a standard computational protocol that effectively balances accuracy and efficiency has yet to be established. To address this, we propose an efficient computational workflow developed through systematic benchmarking. This workflow integrates two key components: an analytical model developed using the SISSO machine learning approach to replace expensive frequency calculations and a configuration screening process based on machine learning potentials to account for the vast number of possible surface terminations. Using this workflow, we efficiently calculate the surface free energies of MFI and FAU zeolites and explore their morphological evolution under dynamic conditions. This study establishes a general and efficient theoretical framework for investigating the thermodynamic properties of zeolite surfaces.
Read moreMolecular mechanism and risk assessment of Rhizoctonia solani resistance to the SDHI fungicide isopyrazam.
Emulsified essential oil-organic acid mixtures in drinking water reduce Salmonella Typhimurium infection and improve intestinal health in broilers