Biology subjects

Meng, L.

Publications and source records attributed to Meng, L..

At least 19 recordsLinked to original sources

bioRxiv2026

BioMod: Biological Module Tokenization for Single-Cell Foundation Modeling

Single-cell foundation models typically represent cells as flat sequences of individual genes, requiring higher-order biological organization to be inferred implicitly from sparse expression profiles. Similar to the evolution from character-level to semantic tokenization in natural language processing,we hypothesize that cellular states can be more efficiently represented using biologically meaningful intermediate units. Here we present BioMod, a 50-million-parameter single-cell foundation model that introduces biological modules as representation units between genes and cells. BioMod constructs an overlapping vocabulary of 660 biological modules derived from curated pathways and data-driven gene programs, replacing thousands of gene-level inputs with compact module representations. Pretrained on approximately 73 million human cells using high-ratio module masking with an asymmetric decoder, BioMod achieves state-of-the-art performance across cell-type annotation, zero-shot batch integration, perturbation-response prediction and drug-response forecasting while maintaining a compact architecture that enables efficient inference on a single GPU. Module-level analyses further demonstrate that BioMod captures biologically meaningful cellular programs and preserves pathway-level organization.

bioinformatics↗

bioRxiv2026

AbRefine: Framework-Conditioned Refinement for Structure-Guided Antibody CDR Design

Structure-guided antibody CDR design constrains residue selection using backbone geometry, but structural evidence alone may leave multiple amino acids plausible. We investigate whether the fixed antibody framework provides complementary sequence information for resolving this ambiguity. We introduce AbRefine, an information-aware fusion framework that combines backbone-conditioned structural predictions with framework-conditioned sequence distributions derived from a pretrained antibody language model with all designed CDRs masked. Its Information-Aware Fusion (IAF) module learns residue-specific fusion weights from the uncertainty, disagreement, and information content of the two predictive distributions, while keeping both pretrained experts frozen. Controlled interventions show that the signal is target specific: matched frameworks outperform shuffled frameworks by 7.37 percentage points, and the largest gain occurs at positions with high structural uncertainty and informative framework evidence (+5.77$ points). Compared with static fusion, IAF further improves AbMPNN recovery by +1.53 points (95\% CI +0.93$ to +2.14$) and significantly reduces native negative log-likelihood for both AbMPNN and AntiFold, without detectable degradation in fold-back structural compatibility. These results show that framework context provides information beyond backbone geometry and that learning its residue-specific utility enables effective adaptive fusion for antibody CDR design.

bioinformatics↗

bioRxiv2026

When label-free morphology is sufficient for targeted cellular measurements

Label-free morphology captures cellular responses, but its ability to substitute for targeted cellular measurements depends on the intended use. We assess measurement sufficiency using nearly 10 million paired phase-reporter observations across 1,000 gene knockouts, 52 fluorescent reporters and 73 A549 screens. Ten predictors differed in recovery across held-out fields, genes and screens. Same-cell pairing controls identified reporter-state information beyond perturbation averages and measured covariates. Perturbation ranking often persisted despite reduced variation in predicted response magnitudes. Predictions of held-out knockout responses retained a median 79% of the strongest hits, whereas functional-term retention varied. Atlas-derived criteria identified 30 quantitative and 7 ranking proxies for a fixed ensemble, with reference reproducibility constraining interpretation. In independent primary-hepatocyte data, brightfield predictions prioritized 10 of the 11 compounds with the largest measured metabolic-activity losses among 217 held-out compounds. Measurement sufficiency therefore depends on target, predictor, context and scientific task, beyond predictive correlation alone.

bioinformatics↗

bioRxiv2026

Discovery and Optimization of Imidazothiazole Carboxamides as Novel Anti-Tuberculosis Agents

Screening of the open-access CRESTdb small-molecule library identified the imidazothiazole carboxamide sCQG200 (1) as an initial hit, with activity against H37Rv and Erdman Mycobacterium tuberculosis strains in cholesterol-containing medium (MIC90= 6.88 uM and 4.48 uM, respectively) and against intracellular Mtb (EC50= 3.80 uM). sCQG200 retained activity against drug-resistant Mtb strains, including clinical MDR/XDR isolates. SAR optimization led to analogs 21 and 24 with substantially improved antimycobacterial potency. Mouse pharmacokinetic studies following oral and intravenous administration showed 62.1% and 29.5% oral bioavailability for 21 and 24, respectively. This structurally differentiated chemotype provides a promising starting point for further optimization as antitubercular agent.

microbiology↗

bioRxiv2026

spAlignDE unifies cross-sample and cross-modal spatial alignment with mismatch-aware differential expression

Comparative analysis of spatial omics requires aligning data across samples and modalities to a common coordinate system. Existing methods can be computationally intensive for large datasets, and cross-modal alignment is difficult when datasets lack comparable molecular features. In addition, residual alignment errors can cause locations assigned to the same coordinates to represent different biological regions, producing false differential expression signals. Here we propose spAlignDE, a computational method that integrates structure-guided spatial alignment with mismatch-aware local differential expression analysis. spAlignDE represents structures from spatial transcriptomics, spatial ATAC-seq, histology, and anatomical atlases as continuous fields and aligns them by shooting-based diffeomorphic registration without requiring shared molecular features. In cross-sample benchmarks against 12 methods, spAlignDE achieved the highest agreement in gene expression patterns and anatomical annotations. It also scaled to 20 MERFISH brain sections containing 1.45 million cells. For cross-modal tasks, spAlignDE accurately aligned spatial transcriptomics with histology, the Allen Mouse Brain Common Coordinate Framework, and spatial ATAC-seq. After alignment, spAlignDE estimates local expression contrasts on a shared grid and inflates their variances according to mismatch risk estimated from putatively stable genes and local observation density. The analysis can also adjust for cell-type composition. Simulations showed improved false discovery control without systematic loss of power. In real-data applications, spAlignDE localized age-associated changes in gene expression and T-cell distribution in the mouse brain and spatially restricted expression differences between normal and injured kidney sections.

bioinformatics↗

bioRxiv2026

A hierarchical orthology framework reveals viral carbohydrate-active genes across the global virosphere

Carbohydrate-active enzymes (CAZymes) shape virus-host interactions by modifying virion structures, host surfaces and extracellular glycans. However, the diversity and evolutionary origins of viral carbohydrate-active enzymes remain poorly understood, partly due to limited viral protein annotations. To address this, we present VirGenes, a database of viral orthologous groups constructed from the KEGG viral gene dataset. VirGenes uses a hierarchical framework that integrates sequence similarity, remote homology, and structural similarity to support evolutionary and functional analyses of viral proteins. By screening the sequence space of VirGenes, we identified 558 CAZyme-associated gene clusters spanning 102 CAZyme families, revealing particularly enriched repertoires in dsDNA viral lineages. Two bacteriophage families, Kleczkowskaviridae and Pootjesviridae, encoded more than 10 CAZymes per genome, followed by Mimiviridae, a representative family of eukaryotic giant viruses. Phylogenetic analyses systematically revealed divergent evolutionary histories of viral carbohydrate-active genes, including frequent horizontal transfer of endolysin genes from bacteria, which likely represents a viral strategy in the ongoing evolutionary arms race with their cellular hosts. Within the structural space of VirGenes, a large number of viral genes were found to contain CAZyme-like folds despite more than 85% of them lacking detectable sequence similarity to annotated CAZyme sequences. Notably, numerous hypothetical sequences from giant viruses exhibited glycoside hydrolase-like five-bladed {beta}-propeller folds. Overall, by integrating sequence, structural and functional evidence, we show that viral carbohydrate-active systems exemplify how distributed innovations, constrained by ancient folds, collectively build the functional complexity of the global virosphere. VirGenes is publicly accessible at https://www.genome.jp/vogdb/.

bioinformatics↗

bioRxiv2026

Individual-tree phenology reveals climate-dependent responses to urban thermal heterogeneity across U.S. cities

Rapid urbanization is altering the seasonal life cycles, or phenology, of urban trees. Diverse species composition and heterogeneous urban thermal environments can generate pronounced phenological variation within cities, yet such fine-scale seasonality remains poorly understood. This limits the ability to anticipate localized ecosystem services and disservices, including canopy cooling and pollen exposure. Here, we analyzed individual-tree phenology and their response to temperature across 76 cities in the contiguous United States by integrating municipal street-tree inventories, PlanetScope satellite time series, and 1-km near-surface urban air-temperature data. We quantified intra-city and cross-city phenological variation, estimated species-level associations between phenology and fine-scale urban temperature, and tested whether these associations vary with regional climatic context. Intra-city phenological variation rivaled cross-city variation for 33.3% of species in spring and 53.7% in fall. Temperature-phenology associations were widespread: warmer local urban environments were associated with earlier spring onset in 51.5% of cases and delayed fall senescence in 66.5%, with approximately two-thirds of these responses cascading to longer growing seasons. These associations varied with regional climate, generally showing stronger spring advancement and fall delay in cooler and wetter cities, but weaker or reversed responses in hotter or drier cities. Together, these results suggest that urban tree phenology is shaped by interactions among fine-scale urban temperature, species identity, and regional climate. Accounting for this heterogeneity can improve predictions of urban forest function and inform climate-resilient species selection and management. Plain Language SummaryStreet trees within the same city do not all leaf out in spring or lose their leaves in fall at the same time. This seasonal timing, called phenology, affects services such as shade and cooling, as well as disservices such as pollen exposure. We studied individual tree phenology and their temperature response in 76 U.S. cities using street-tree records, satellite observations, and local air-temperature data. We asked how much phenology varies within cities, how it responds to neighborhood-scale temperature differences, and whether these responses depend on regional climate. Variation within a city was often as large as variation among cities, especially in fall. Trees in warmer parts of cities generally leafed out earlier and lost their leaves later, often extending the growing season. However, these responses were stronger in cooler and wetter cities and weaker or sometimes reversed in hotter or drier cities. These findings show that urban tree seasonality depends on local temperature, species identity, and regional climate, which should be considered when selecting and managing trees for future cities. Key PointsO_LISubstantial within-city phenological variation is not captured by city-level averages. C_LIO_LIFine-scale temperature shaped phenology and growing-season length, but responses varied across species, cities, and phases. C_LIO_LITemperature sensitivity depended on regional climate, weakening or reversing in hotter or drier cities. C_LI

ecology↗

bioRxiv2026

Insect-inspired, efficient event-based classification of tactile features

Tactile sensing enables humans and animals to detect and discriminate features during exploration and guide context appropriate actions. Compared to conventional touch sensors, sensing of tactile features in animals is fundamentally event-based through spikes. Yet how sensor mechanics shape spike activity for tactile perception is not well understood. Inspired by the American cockroach--an insect touch specialist--we developed a neuromechanical framework that linked antenna passive mechanics, mechanosensory encoding, and spike-based computation. A physics-based model of antenna bending simulated spatiotemporal strain patterns during contact, which were encoded into spike trains through a strain-to-firing mapping calibrated against electrophysiological recordings. The model captured antennal nerve activity observed in vivo by reproducing key features of population-level neural responses across multiple contact locations and speeds. Compared with conventional threshold-based encoding, the insect-inspired spike encoder preserved the spatiotemporal structure of tactile signals while achieving sparser activity. To establish a link between spiking activity and perception, we trained a spiking neural network to classify contact location and speed directly from the predicted spike trains. The network achieved >95% accuracy with reduced computational demands and enabled rapid discrimination within the first 170 ms of contact, indicating that sparse, event-based codes support fast and reliable tactile perception. Together, these results establish a mechanistic bridge between sensor mechanics and neural computation, revealing how physical interactions shape efficient sensory coding. This integrative framework advances our understanding of tactile perception and provides design principles for energy-efficient, neuromorphic tactile systems. Author SummaryAnimals use touch to explore their surroundings, identify objects, and make rapid decisions. Unlike most engineered touch sensors, which continuously transmit data, biological touch systems communicate through brief electrical signals called spikes. However, how the physical properties of a touch sensor influence these signals remains poorly understood. In this study, we used the antenna of the American cockroach as a model system to investigate how mechanics and neural activity work together during touch. We developed a computational framework that links the way an antenna bends during contact to the neural signals generated by touch-sensitive sensors. By comparing our model with neural recordings from living insects, we showed that it can reproduce key patterns of neural activity observed during tactile interactions. We found that the insect-inspired encoding strategy produces sparse signals that retain important information about where and how contact occurs. These signals enabled a neural network to rapidly and accurately identify contact location and speed while using fewer computational resources. Our results suggest that tactile perception emerges from a close interaction between sensor mechanics and neural processing. Beyond advancing our understanding of animal sensation, this work provides principles for designing energy-efficient touch sensors and neuromorphic robotic systems.

neuroscience↗

bioRxiv2026

The in vivo inhibitory function of the MHC-I alpha3 domain/CD8alpha interaction

The interaction between the Major Histocompatibility Complex Class I (MHC-I) 3 domain and CD8 has classically been viewed as a positive coreceptor interaction that stabilizes TCR signaling during antigen recognition. However, its physiological function in mature peripheral CD8+ T cells in vivo remains incompletely understood. Here, we identify the MHC-I 3 domain-CD8 interaction as a previously unrecognized inhibitory pathway that tonically restrains peripheral CD8+ T-cell activation and maintains T-cell tolerance in vivo. Antibody-mediated disruption of the MHC-I 3 domain-CD8 interaction induced spontaneous activation of peripheral CD8+ T cells without impairing their survival, lowered the threshold for antigen-induced activation, and enhanced responsiveness to cognate peptide stimulation. In peptide-induced OT-I T-cell anergy models, blockade of either H-2Db or H-2Kb 3 domain interactions with CD8 prevented the induction of anergy and restored responsiveness of previously anergic T cells. Notably, blockade of the H-2Kb 3 domain enhanced OT-I responses despite simultaneously disrupting the classical positive coreceptor interaction within the TCR-peptide-MHC complex, indicating that tonic inhibitory signaling mediated by the MHC-I 3 domain predominates under these conditions. Together, these findings redefine the classical MHC-I-CD8 interaction as a bidirectional pathway that not only supports antigen recognition but also imposes tonic inhibitory control over peripheral CD8+ T cells. These results identify the MHC-I 3 domain-CD8 axis as a potential target for reversing T-cell tolerance and enhancing antitumor or antiviral immunity.

immunology↗

bioRxiv2026

Eleven deep-sea coral genome assemblies unveil insights into evolution, adaptation, and coral biodiversity

Deep-sea corals are vital in maintaining coral ecosystem biodiversity, yet their genetic characteristics remain largely unexplored. Here, we present 11 deep-sea coral genome assemblies, including four Hexacorallia and seven Octocorallia species, significantly contributing new genomic information across two orders. Our analysis reveals the historical dynamics of coral speciation and the influence of environmental factors on the evolution of coral reef ecosystems.Total of 126 horizontal gene transfer (HGT) events were detected, among which genes from the ancestor of symbiodiniaceae indicate that the ancestors of deep-sea corals may have inhabited shallow-sea environments. Notably, several of these HGTs are involved in phosphorus (PhnX/PhnW) and cholesterol (DHCR7) metabolisms within corals, indicating that HGTs may serve as an adaptive survival strategy for the coral holobionts. Deep-sea corals also rely on symbiotic bacteria to synthesize 10 essential amino acids (such as valine and tyrosine), retaining only partial amino acid synthesis capacity. In addition, we investigated the evolution of key biological rhythm genes and temperature adaptation in corals. The loss of key rhythm genes (e.g., clock and cry) in deep-sea corals and copy number difference of genes related to heat stress (e.g., Cbl-b and Rchy) revealed genetic difference between deep-sea and shallow-sea corals. Our new genome assemblies enhance the understanding of deep-sea coral evolution, biodiversity, and adaptation, providing a genetic foundation for coral conservation.

genomics↗

bioRxiv2026

Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells

Cohesin is crucial for establishing 3D genome organization and functions. However, the in vivo mechanism of cohesin-mediated extrusion remains unsettled. Here, we investigated extrusion directionality using integrated genome mapping coupled with perturbation in human cells. By defining cohesin loading at NIPBL binding loci and anchoring at CTCF sites, we systematically characterized the aggregated and single-molecule trajectories of extrusion "stripes" and contact "dots" from and between individual cohesin loading and anchoring points. Our analyses delineated two dynamic modes of in vivo mechanism in which NIPBL/cohesin initiates extrusion at its loading sites in a one-sided manner; after encountering CTCF, CTCF/cohesin switches its extrusion direction backward and robustly extrude DNA unidirectionally until completing the convergent CTCF loop. Surprisingly, depleting CTCF resulted substantial increase of NIPBL/cohesin-mediated extrusion activity, which is further validated by in silico perturbation. These findings reveal novel mechanistic insights into how cohesin and CTCF orchestrate cohesin-mediated loop extrusion in vivo.

genomics↗

bioRxiv2026

ExMODE: A Multi-Omics Repository for Extremophile Adaptation and Bioprospecting

Extreme environments, though hostile to most life forms, host specialized extremophile communities that have redefined biological cognition and emerged as vital biotechnological resources, with their unique adaptive traits and bioactive molecules driving advances in multiple scientific and industrial fields. However, research on extremophiles is hindered by limitations in culture-based methods, fragmented multi-omics data with non-uniform annotation standards across repositories, the lack of cross-extreme comparative research in existing resources, and the singularity of data dimensionality that neglects key structural information, all of which restrict the functional interpretation of extremophile microbes and the exploitation of their bioprospecting potential. To tackle these challenges, we developed ExMODE (https://db.genomics.cn/exmode/), a comprehensive multi-omics database platform dedicated to extremophiles. It centrally integrates multi-omics data from diverse extreme habitats with a standardized annotation framework, resolving data fragmentation and enabling systematic cross-environment comparative analyses to elucidate extremophile adaptive mechanisms. Moreover, ExMODE aggregates multi-dimensional datasets including genes, genomes, secondary metabolite sequences and protein structures, overcoming the constraints of single-dimensional data and significantly improving the efficiency of biotechnological resource discovery from extreme microorganisms.

microbiology↗

bioRxiv2026

Developmental Elimination of Electrical Synapses by UNC-51/UNC-76-Mediated Vesicular Transport

Neural circuit maturation requires precise elimination of transient synaptic connections, but how electrical synapses are eliminated remains unknown. Using C. elegans PLM mechanosensory neurons, we found that gap junctions form transiently during early development and are subsequently eliminated as the circuit matures. These transient electrical synapses drive high-frequency calcium oscillations, and optogenetic ablation of early gap junctions abolishes calcium dynamics and disrupts chemical synapse formation, demonstrating their critical developmental function. Through forward genetic screening, we identified the conserved kinase UNC-51/ULK as essential for elimination. UNC-51 phosphorylates the kinesin adaptor UNC-76/FEZ to initiate RAB-10-dependent retrograde trafficking, progressively depleting innexin proteins from the synaptic site. Disrupting this pathway prevents elimination, causing persistent electrical synapses and neuronal hyperactivity. These findings establish a conserved framework for developmental elimination of functionally essential transient electrical connectivity.

cell biology↗

bioRxiv2026

Mitochondria Organize Gap Junctions to Enable Neural Circuit Scaling

Neural circuits must maintain function during dramatic growth-driven expansion. While chemical synapses can be independently reorganized in pre- and postsynaptic neurons, gap junctions physically couple partner cells, requiring coordinated spatial redistribution--a process whose mechanisms remain unknown. Using the C. elegans mechanosensory circuit, we show that gap junctions undergo stereotyped developmental reorganization, transitioning from clustered to dispersed configurations as partner neurites elongate. Forward genetic screening identified RIC-7, a mitochondrial adaptor protein, as essential for this redistribution. Loss of RIC-7 prevents gap junction dispersal, trapping partner neurites at clustered sites and severely impairing electrical transmission. Mechanistically, RIC-7 directs mitochondrial positioning to gap junctions, where mitochondria recruit the microtubule-organizing component PTRN-1 to locally enhance microtubule dynamics. Disrupting mitochondrial transport (miro-1;mtx-2 mutants) or PTRN-1 function phenocopies ric-7 defects, while metabolic dysfunction does not, establishing a non-metabolic role for mitochondria in organizing synaptic architecture. Remarkably, RIC-7 expression in one neuron alone suffices to restore gap junction and partner neurite distribution across both coupled cells. Structural modeling suggests mechanical adhesion between docked hemichannels enables this coordinated reorganization. These findings establish mitochondria as mobile organizers of synaptic spatial architecture, demonstrate that proper junction distribution is essential for electrical transmission efficacy, and reveal how cell-autonomous mechanisms can achieve bilateral structural coordination during circuit growth.

neuroscience↗

bioRxiv2026

Promoter editing of starch branching enzyme IIb and granule-bound starch synthase I balances resistant starch content and amylose content in rice

Increasing attention is being focused on the glycemic index (GI) of daily food for humans, and the resistant starch content (RSC) is an important indicator of GI for starch-rich staple foods. In recent years, some studies revealed that the loss function of single or multiple key enzymes in the primary pathway of starch synthesis substantially increases RSC in rice, such as starch branching enzyme IIb (BEIIb) and soluble starch synthase IIIa (OsSSIIIa). However, a noteworthy negative characteristic of these high RSC mutants is the substantially increased amylose content (AC). AC as a major determinator of rice eating quality, must not be higher than an acceptable limit for most consumers. To solve this problem, in this study, we adopted two promoter editing (PE) editing strategies to develop rice germplasms with a better balance of RSC and AC: one is to edit the promoter of BEIIb in a low AC rice variety, another is to edit the promoter of Waxy (Wx) gene in a BEIIb loss of function mutant. Using AC[≤]20%, which is the range of premium quality rice in China as a criteria, we finally obtained 2 homozygous lines with significantly increased RSC ([≥]5%) in the NG46 background by promoter editing of BEIIb and 1 homozygous line in the YouTang2 (YT2, a BEIIb mutant) background by promoter editing of Wx gene. Further analysis revealed that AC and the amount of long-chain branches of amylopectin are positively correlated with RSC in the population of BEIIb PE lines. However, unexpectedly, the Wx PE-line with substantially decreased AC (17.7%) also showed significantly increased RSC (16.9%). Our study not only produces useful germplasms for the high RSC rice breeding in the future but also provides an insight into understanding the relationship between AC and RSC in defective BEIIb rice.

plant biology↗

bioRxiv2026

Rapid diversification of a natural Heterosigma akashiwo virus population during a host bloom

Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Most knowledge on their population genetic dynamics is derived from a small number of laboratory-based experiments, whereas patterns in nature are rarely observed. To overcome this limitation, we traced genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan, by integrating cell counting, metabarcoding, metagenomic and metatranscriptomic sequencing. Our study revealed that HaV dominated the giant virus community in most samples, with the relative abundances of up to 56%. Despite the high abundances, the HaV population exhibited a relatively low level of microdiversity but with a high pN/pS ratio compared to other giant viruses in the study site. Microdiversity increased during the early sampling period, reached a maximum at mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, possibly driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Together, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variation.

ecology↗

bioRxiv2026

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

bioRxiv2026

Prime-InDel version 1: A web tool providing InDel markers for targeted regions narrowing

While high-density SNP genotyping enables genome-wide assays in rice (Oryza sativa L.) and other crops, PCR-based markers--particularly those derived from insertion-deletion (InDel) variations--remain crucial for fine-mapping. Currently, readily available primer information for high-density InDel rice markers is still limited. We present the first version of PrimeInDel (https://rfgb.rmbreeding.cn/search/variation/primeIndel), an online tool integrating three sets of InDel markers: an 8K-set and a 316K-set from the 3K Rice Genomes (3K-RG) project, and a 22K-set compiled from published literatures. In user cases, primers from PrimeInDel proved highly effective, narrowing a cold-tolerance QTL (qSR2) from 2.7 Mb to 200 kb and a heading-date QTL (qDeh1.1) from 239.5 kb to 83.6 kb. Our work provides the community with a robust, PCR-based InDel primer, accessible via an online data set, which will facilitate germplasm genotyping and gene identification in rice breeding.

plant biology↗