Hair follicle stem cells (HFSCs) are critical for hair follicle (HF) morphogenesis and cyclic hair regeneration. Periostin (POSTN), an extracellular matrix protein involved in tissue development and skin cell regulation, remains poorly characterized in HFSCs. In this study, we constructed CRISPR/Cas9 vectors targeting POSTN and validated their editing efficiency in primary HFSCs. POSTN editing significantly suppressed cell proliferation and promoted apoptosis. Transcriptomic analysis identified 988 differentially expressed genes (DEGs) enriched in immune responses and MAPK, PI3K–Akt, and cAMP pathways. Metabolomic analysis revealed 98 differential metabolites (DMs) associated with nucleotide metabolism and FoxO, AMPK, and cAMP pathways. Integrated multi-omics analysis showed extensive correlations between DEGs and DMs, and highlighted the cAMP pathway as the core regulatory axis. Western blot (WB) validation confirmed that POSTN editing reduced PKA and CREB phosphorylation, indicating inhibition of the cAMP/PKA/CREB signaling. These findings demonstrate that POSTN regulates HFSCs’ proliferation and apoptosis partially via the cAMP/PKA/CREB pathway, providing novel insights into the functional regulation of HFSCs.

Hair follicle (HF) morphogenesis, growth, and regeneration are fundamentally governed by reciprocal interactions between the epidermal and dermal compartments of the skin, with dermal papilla cells (DPCs) serving as a central regulatory element in this process. Here, the functional role of Toll-like receptor 2 (TLR2) in the control of DPC proliferation was investigated. The coding sequence (CDS) of the rabbit TLR2 gene was successfully cloned and subjected to preliminary bioinformatics analyses to characterize its predicted structural and functional features. Gain- and loss-of-function experiments demonstrated that modulation of TLR2 expression significantly altered the transcription of HF growth- and development-associated genes, including BCL2, CCND1, CTNNB1, FGF2, and TGFβ. Functional assays, including CCK-8 proliferation analysis, EdU incorporation, and immunostaining for proliferating cell nuclear antigen (PCNA), consistently showed that TLR2 overexpression markedly enhanced DPC proliferation, whereas TLR2 knockdown exerted a pronounced inhibitory effect. These results provide mechanistic insight into the role of TLR2 in regulating DPC proliferation and offer a theoretical basis for further investigations into its contribution to hair follicle biology.

Leaf adaxial-abaxial polarity is fundamental for plant morphogenesis and environmental adaptation through asymmetric cell differentiation. Emerging evidence reveals dorsoventral metabolic gradients act downstream of transcriptional networks to fine-tune cellular specialization. While conserved transcription factors (e.g., HD-ZIP III and KANADI) establish initial polarity, the molecular networks driving position-specific cellular differentiation and their integration with metabolic adaptation remain unclear. Leveraging single-nucleus and spatial transcriptomics, we resolve major cell classes (mesophyll, epidermal, and vascular-associated) and their adaxial-abaxial subtypes, revealing dorsoventral polarity in transcriptional profiles and metabolic pathways. Adaxial cells are enriched in phenylpropanoid/flavonoid biosynthesis, while abaxial cells show preferential activation of stress and hormone signaling. Notably, we identify MYC2 as a key regulator of adaxial cuticle biosynthesis, binding to promoters of lipid biosynthetic and transport genes (e.g., CER10 and LTPG1) and promoting cuticle thickening. Our study uncovers how positional identity shapes transcriptional and metabolic polarity in leaves, with MYC2 emerging as a central regulator coordinating organ-specific adaptations. These findings provide insights into the spatial regulation of plant development and stress resilience, offering potential strategies for engineering stress-tolerant woody crops.

Hair-follicle development is a key determinant of the quality and yield of Angora rabbit wool. Vitamin E (VE) has antioxidant properties and regulates cell proliferation. However, the molecular mechanism by which VE regulates hair-follicle growth is unclear. This study investigated the effects of VE on hair follicles and dermal papilla cells (DPCs) in vitro, as well as their underlying regulatory mechanism involving long noncoding RNA (lncRNA)2919, STAT1, and the Hedgehog signaling pathway. Hair follicles and DPCs were isolated and cultured. The optimal VE concentration was determined to be 50 μM. Reverse-transcription quantitative PCR, Western blotting, and CCK-8, DNA pulldown, chromatin immunoprecipitation, and dual-luciferase reporter assays revealed that VE significantly promoted both hair-follicle growth and DPC proliferation, and also regulated the expression of hair follicle-development-related genes, such as LEF1, FGF2, TGFβ1, and SFRP2, and antioxidant genes, including SOD1 and NRF2, and also enhanced the antioxidant capacity. Mechanistically, VE significantly downregulated lncRNA2919 expression, while lncRNA2919 overexpression inhibited DPC proliferation, which was reversed by VE. Furthermore, lncRNA2919 maintained STAT1 protein levels by inhibiting the proteasome-mediated degradation pathway. STAT1 was observed to bind directly to the SHH promoter and inhibit its transcription. This effect was reversed by VE via downregulation of lncRNA2919/STAT1 and subsequent activation of the Hedgehog signaling pathway. In conclusion, VE induces the proliferation of DPCs and enhances cellular antioxidant capacity by regulating the lncRNA2919/STAT1/SHH axis, thereby promoting hair-follicle growth and development. The findings provide a novel theoretical basis for understanding hair-follicle growth and the use of VE in Angora rabbits.

The rapid expansion of single-cell RNA sequencing (scRNA-seq) has made accurate cell type annotation a critical bottleneck for biological discovery. Existing computational methods are often limited by reference data dependency, while emerging single Large Language Model (LLM) approaches are susceptible to model-specific biases and provide insufficient uncertainty quantification. To address these limitations, we introduce mLLMCelltype, a framework that harnesses collective intelligence-the emergent problem-solving capacity arising when multiple independent agents interact through structured deliberation to produce solutions exceeding individual capabilities-of multiple LLMs through an iterative deliberation process. Across 49 diverse datasets, our framework achieves a mean accuracy of 77.2%, a 15.7-percentage-point improvement over the best-performing single-LLM baseline (61.5%). The consensus mechanism demonstrates high robustness to noisy input and generalizes to datasets released after the LLMs' training. By providing transparent reasoning chains and robust consensus-based confidence metrics, mLLMCelltype minimizes manual annotation effort and enables reliable interpretation of complex cellular landscapes. The framework is available as an open-source package and an accessible web server.

OASL, a distinctive member of the 2'-5'-oligoadenylate synthetase (OAS) family, is a well-characterized interferon-stimulated gene (ISG). In mammals and certain avian species, OASL exhibits dual functions in antiviral defense and innate immune regulation. However, the biological role of chicken OASL (chOASL) remains poorly understood, largely due to the natural absence of RIG-I in chickens. Infectious bronchitis virus (IBV) belongs to Gammacoronavirus genus and causes substantial economic losses in the global poultry industry. To explore whether chOASL is involved in the host defense against IBV, this study aimed to comprehensively characterize its expression dynamics and antiviral function. Firstly, the anti-chOASL polyclonal antibody was generated using prokaryotically expressed recombinant protein. Using this validated tool, we demonstrated that endogenous chOASL was significantly induced by Poly(I:C) and QX-IBV in various chicken cells. Furthermore, we mapped the baseline tissue distribution of chOASL protein for the first time and proved that chOASL was markedly upregulated, particularly in immune organs and IBV target tissues during IBV infection. Importantly, overexpression and knockdown assays verified that chOASL could suppress IBV replication. In conclusion, this study not only provides a reliable tool for detecting chOASL but also establishes its specific expression profile and direct antiviral activity against IBV, laying a solid foundation for further elucidating antiviral mechanisms of chOASL.

Spatial transcriptomics has transformed our ability to study tissue architecture at molecular resolution, yet analyzing these data demands navigating dozens of computational methods across incompatible Python and R ecosystems-forcing researchers to devote more effort to making tools function than to pursuing biological questions. We present ChatSpatial, a platform in which the LLM selects from pre-validated tool schemas rather than generating free-form code, with domain expertise embedded in schema descriptions for context-aware parameter inference. Built on the Model Context Protocol (MCP), ChatSpatial unifies 60+ methods across 15 analytical categories into a single conversational workflow spanning Python and R ecosystems. Replication of two published studies-recovering subclonal heterogeneity in ovarian cancer and tumor microenvironment organization in oral squamous cell carcinoma-and validation across seven LLM platforms demonstrate that schema-enforced orchestration yields near-deterministic reproducibility at the workflow level for multi-step spatial analyses. Beyond replication, exploratory cross-method analyses illustrate practical triangulation across independent analytical frameworks.

To elucidate the paracrine regulatory mechanism of dermal papilla cells (DPCs) on melanocyte (MC) melanogenesis, we focused on exosomal miR-199a-3p as a key mediator. DPCs, MCs, and DPC-Exos were identified by immunofluorescence, Western blot (WB), nanoparticle tracking analysis (NTA), and transmission electron microscopy (TEM). Functional assays showed DPC-Exos were internalized by MCs, enhanced proliferation, decreased apoptosis, and elevated melanin production. miRNA sequencing identified miR-199a-3p as the key exosomal cargo, which was localized to hair follicle bulbs by fluorescence in situ hybridization (FISH). Transwell co-culture and Cy3-tracing revealed intercellular transfer. Dual-luciferase assays confirmed miR-199a-3p directly targets the 3'UTR of POU2F1. Additionally, exosomal miR-199a-3p promoted the growth of ex vivo hair follicles and significantly regulated the expression of melanogenesis-related genes in hair follicles. Gain-of-function experiments demonstrated that DPC-Exos transfected with miR-199a-3p mimics suppressed POU2F1, effectively reversing its anti-melanogenic activity. This study elucidates an exosome-mediated DPC-MC regulatory axis centered on miR-199a-3p/POU2F1, providing novel therapeutic targets for pigmentation disorders and advancing animal coat color modulation strategies.

Methods that map genetic risk to cells do not directly test whether spatially organized ligand-receptor (LR) gene annotations carry conditional heritability association. Here we introduce EdgeMap, which scores each gene by the spatial activity of its LR contexts in spatial transcriptomics data, maps these scores alongside cell-intrinsic annotations to SNP-level LD scores, and tests both jointly against GWAS summary statistics. Across 17 traits and five human tissues, edge z -scores are systematically higher in biologically matched tissues: all 15 traits with both matched and unmatched tissue classes show this ordering (median Δ z = 1.51 ; sign P = 3.1 × 10 -5 ), and 11 of 13 nominal-positive associations concentrate in the biologically matched set ( P = 1 × 10 -4 ). The pattern survives broad LR-gene-class and cell-type composition controls. Donor-level cross-section summaries, independent GWAS replication for LDL and CAD, and cell-segmented Visium HD liver data provide convergent support. A secondary analysis prioritizes constituent genes within active LR contexts; sixteen of 31 prioritized genes are absent from standard gene-level methods. These results establish spatially weighted LR-gene annotations as a complementary layer for interpreting complex-trait genetic architecture.

Identifying spatially variable genes (SVGs) is the first analytical step in spatial transcriptomics, determining which genes and pathways are prioritized for downstream validation. Yet the restricted spatial models of current detection methods create systematic blind spots that can exclude biologically coherent programs from discovery. Here we present FlashS, which reformulates kernel-based spatial testing in the frequency domain to detect arbitrary multi-scale expression patterns while scaling to millions of cells. In human cardiac tissue, this broader detection capacity recovers a coherent PGC-1α-regulated mitochondrial biogenesis program-40 of 49 pathway genes spatially associated with ventricular cardiomyocytes-that PreTSA, a leading parametric alternative, largely misses (1 of 49 genes), a finding replicated in an independent cohort. Across 50 benchmark datasets spanning 9 platforms, FlashS achieves state-of-the-art ranking accuracy (mean Kendall τ = 0.935 ) and completes on the Allen Brain MERFISH atlas (3.94 million cells) in 12.6 minutes with 21.5 GB memory.

To elucidate variations in meat quality of rabbits at different developmental stages, we investigated phenotypic traits, metabolites, and gene expression profiles in the longissimus lumborum (LL) muscle at three ages (M1, M3, and M5). Carcass evaluation revealed the period from 1 to 3 months (M1-M3) constitutes the rapid growth phase, and both full-eviscerated and semi-eviscerated dressing percentages tended to stabilize after M3. Rabbits in group M1 showed significantly higher cooking loss, pH after 24 h (pH 24), lightness (L*), and yellowness (b*) (P < 0.01) and significantly lower shear force (P < 0.05) compared with those in the M3 and M5 groups. LC-MS/MS profiling of rabbits in the M1, M3, and M5 groups identified dynamic fluctuations in critical metabolites, including amino acid derivatives (anserine, aspartic acid, L-Glutamic acid, small peptides), glycerophospholipids (LPE, LPA), and energy regulators (oxaloacetate, fumaric acid), collectively modulating related key attributes of meat quality including tenderness, flavor, and oxidative stability. Integrated analyses identified correlations involving key factors such as oxaloacetic acid, betaine and some peptides, which were correlated with genes including PCK2, MYO10, and ANKRD44, indicating synergistic effects on meat quality. These findings offer insights into the assessment and regulatory mechanisms of rabbit meat quality.

This study assessed meat quality in two rabbit cuts, the longissimus lumborum (LL) and hind-leg muscle (HL), from Yongqing Rex rabbits using integrated lipidomic, metabolomic, and proteomic approaches. We investigated the influence of fat content on the flavor characteristics of these cuts. Solvent extraction and Oil Red O staining revealed significantly higher intramuscular fat levels in LL than in HL, establishing a compositional basis for flavor differences. Lipidomic analysis identified 663 differentially abundant lipids enriched in glycerophospholipid metabolism and metabolic pathways. Metabolomic profiling identified 179 differential metabolites, including carnosine, L-isoleucine, ornithine, and PC(18:0/18:2), significantly upregulated in LL. Proteomic analysis revealed 171 differentially expressed proteins associated with glycine, serine, and threonine metabolism. Integrated multi-omics analysis further demonstrated substantial differences between LL and HL in pathways including protein digestion and absorption, glycerolipid metabolism, and steroid biosynthesis. These results clarify determinants underlying differences in meat quality between LL and HL muscles in rabbits.

Phospholipase c-delta 1 (PLCD1), a key effector in the phospholipid signaling pathway, is indispensable for the growth and development of hair follicles (HF), but its regulatory mechanism in dermal papilla cells (DPCs), the core functional cells of HF, remains unclear. In this study, a PLCD1 knockout rabbit DPC in vitro model (PLCD1-/-) was successfully constructed using CRISPR/Cas9 gene editing. PLCD1 knockout led to notable impairment of DPC physiological functions. Moreover, through transcriptome and metabolomics analyses, we examined differences in gene and metabolite profiles of DPCs between PLCD1-/- and wild-type (WT) groups, and performed an integrated association analysis of all differentially expressed genes (DEGs) and differential metabolites (DMs). The results showed widespread and significant positive and negative correlations between the screened DEGs and DMs, revealing a closely coordinated regulatory network between the transcriptome and metabolome at the global level after PLCD1 knockout. The functional status of the Hypoxia inducible factor-1 (HIF-1) and Mitogen activated protein kinase (MAPK) signaling pathways was further analyzed by Western blotting. The results showed that PLCD1 deficiency significantly affected the expression levels and phosphorylation status of key proteins in these two pathways. In summary, this study confirmed that PLCD1 deficiency impairs DPC function by inhibiting the HIF-1/MAPK signaling pathway, and the mechanism depends on the PLCD1-regulated gene-metabolite interaction network. This study provides an important theoretical basis for analyzing the regulatory mechanisms of HF growth and development and clarifies that PLCD1 and its downstream gene-metabolic network may serve as potential therapeutic targets for hair-related diseases.

Granulosa cells (GCs), as the largest proportion of somatic cells in mammalian ovarian follicles, play a central regulatory role in follicular development and oocyte maturation. In-depth analysis of the molecular mechanisms related to the growth and development and functional regulation of GCs is of great significance for improving the regulatory network mechanism in the field of female reproduction. Kruppel Like Factor 12 (KLF12) gene is involved in the regulation of various cellular physiological activities, but its specific regulatory function in ovarian GCs is not yet clear. In this study, the coding sequence (CDS) of KLF12 gene in New Zealand female rabbits was cloned for the first time, and the expression abundance and cellular localization of this gene in ovarian tissues of female rabbits at different reproductive stages were systematically analyzed. The results showed that KLF12 was highly expressed in the ovaries of 18-month-old female rabbits. Functional studies found that overexpression of KLF12 significantly inhibited the synthesis of Estradiol (E2) and Progesterone (P) in GCs, and the expression of genes related to cell proliferation, apoptosis and cycle development also changed. Further Western blot (WB) detection confirmed that KLF12 overexpression significantly reduced the phosphorylation levels of key molecules PI3K and Akt in the PI3K/Akt signaling pathway, while KLF12 knockdown had the opposite effect on GCs function. These results reveal the molecular mechanism of KLF12 regulating the development and function of ovarian GCs in New Zealand female rabbits through PI3K/Akt signaling pathway, which not only provides a theoretical basis for improving the reproductive performance of female rabbits, but also provides a new scientific perspective for the study of the molecular mechanism of mammalian reproductive regulation.

The giant freshwater prawn (Macrobrachium rosenbergii) is a commercially pivotal crustacean species in global freshwater aquaculture, while vibriosis caused by non-O1 Vibrio cholerae has become the primary bottleneck restricting its sustainable intensive farming. Vitamin D3 (VD3) is a biologically active fat-soluble nutrient involved in mineral metabolism and immune regulation in animals, yet its effects on the physiological responses of M. rosenbergii under a pathogenic bacterial challenge remain largely unelucidated. In this study, six experimental diets were formulated with graded dietary VD3 concentrations (0.10, 0.18, 0.28, 0.48, 0.68, and 0.88 mg/kg) to feed juvenile M. rosenbergii (initial body weight: 2.06 ± 0.07 g) for 70 d, followed by a 72 h non-O1 Vibrio cholerae challenge test. The results showed that dietary VD3 supplementation alleviated the non-O1 Vibrio cholerae-induced histopathological damage in the intestine and hepatopancreas of prawns. VD3 supplementation significantly modulated antioxidant enzyme activities in a tissue-specific manner: SOD activity increased in the intestine, while CAT and GSH-PX activities increased in the hepatopancreas. However, the MDA, T-AOC, and GSH-PX (intestine) or SOD (hepatopancreas) showed no significant responses, indicating that VD3's antioxidant effects were selective rather than comprehensive. Meanwhile, an appropriate amount of VD3 markedly upregulated the mRNA expression of multiple immune-related genes (pattern recognition receptors, antimicrobial peptides and immune effectors) in a tissue-specific pattern. However, some antioxidant indices and immune-related genes showed no significant responses. Furthermore, VD3 supplementation significantly modulated certain muscle physicochemical parameters of prawns, including altered redness, cooking loss, and textural characteristics. Based on the evaluated physiological indicators, 0.48-0.68 mg/kg VD3 appeared to produce the most favorable overall response. These findings suggest that dietary VD3 may modulate the physiological responses associated with host defense during a bacterial challenge in M. rosenbergii, potentially through modulation of antioxidant capacity and immune-related gene expression, while benefiting the flesh quality. VD3 is thus a potential nutritional approach for improving health status during a bacterial challenge in freshwater crustacean farming.

Rex rabbit fur is a high-value material in the textile industry; however, the integrated metabolomic and transcriptomic mechanisms underlying differences in fur traits between fur-type Rex rabbits and meat-type New Zealand White rabbits remain incompletely understood. In this study, 40 rabbits (20 per group) raised under identical feeding conditions were used to evaluate fur quality traits. Dorsal skin samples were collected for metabolomic and transcriptomic analyses. The results showed that Rex rabbits had significantly lower fibre length and fur thickness than New Zealand White rabbits (p < 0.01). Metabolomic analysis identified 267 DMs, mainly comprising lipids and organic acids. These metabolites were enriched in butanoate metabolism, steroid hormone biosynthesis, cysteine and methionine metabolism, and the citrate cycle. Key metabolites included histamine, L-arginine, creatine, and indoxyl. Transcriptomic analysis identified 895 DEGs, enriched in MAPK, cAMP, and HIF-1 signaling pathways, including keratin family genes (KRT34, KRT84, KRT82), FGFR4, EGF, BMP5, and DKK2. Integrated analysis identified 211 DEGs and 97 DMs co-enriched in 103 pathways, including HIF-1, cAMP, and AMPK signaling pathways. These findings reveal a gene–metabolite regulatory network involved in skin and hair follicle development, provide molecular markers for improving rabbit fur quality, and enhance understanding of the genetic and metabolic basis of mammalian hair follicle development.

High-fidelity three-dimensional (3D) reconstruction enables the fine-grained phenotypic analysis and the establishment of digital twins of the pepper plug tray seedlings. Rowed seedlings in trays with tight interval poses significant challenge to multi-view 3D reconstruction. Previous investigations were largely restricted to the reconstruction of individual seedlings or the estimation of large-scale phenotypic traits of populations. In this study, a prototype with a multi-camera array was proposed to rapidly collect multiview dataset of pepper plug seedlings via row-scanning imaging. 2D Gaussian Splatting (2DGS), a cutting-edge 3D reconstruction approach based on novel view synthesis (NVS), was introduced to extract geometrically accurate mesh of pepper plug tray seedlings. In comparison to other multi-view 3D reconstruction methods, 2DGS yielded high-fidelity meshes with superior overall performance, achieving a competitive average chamfer distance error below 0.88 mm. Incorporated with PlantNet, a deep learning network for plant point cloud segmentation, sections of meshes were smoothly segmented and reassembled into independent seedling instances, providing reliable prerequisites of organ-level trait measurement. The proposed solution yielded the mean absolute percentage errors (MAPEs) of 0.91%, 2.67%, 3.88%, 4.95% in prediction of seedling height, main stem length, leaf blade length and leaf blade area, respectively. This study verified the accuracy and effectiveness of the proposed row-scanning solution on pepper seedlings, promoting the development of high-throughput phenotyping equipment for plug tray seedlings in production.

Rex rabbit fur quality determines economic value, yet the age-dependent dynamics of hair follicle development and their molecular drivers are largely unknown. Here, we performed a time-series integrative analysis combining phenotypic measurements, quantitative histomorphology, and transcriptome sequencing in Yongqing Rex rabbits across 1 to 6 months of age (10 rabbits per month). Fur thickness exhibited a pattern of increase, stabilization, and subsequent increase, with no significant differences between 2M and 4M (p > 0.05). Coat density peaked at 6M, with an average pelt area of 1358.20 ± 52.43 cm2 at 5M and 6M. Fiber length increased and then plateaued, whereas hair diameter showed an increase-decrease-stabilization pattern. Histological analysis revealed a significant age-related decrease in the number of follicle clusters, particularly from 1M to 3M (p < 0.05). Primary hair follicle density was the highest at 1M (p < 0.01) and fluctuated subsequently, whereas secondary hair follicle density increased continuously (p < 0.01). Melanin granules increased significantly from 1M to 4M and peaked at the 4M (p < 0.05). Further, transcriptomic identified 1168, 4204, and 3431 differentially expressed genes (DEGs) for 3M versus 1M, 5M versus 1M, and 5M versus 3M, respectively, with 187 common DEGs including FOXN1, FGF10, and DCN. GO and KEGG analysis indicated significant enrichment in processes such as keratinization, keratinocyte differentiation, ECM-receptor interaction, and the PI3K-Akt signaling pathway. Collectively, our findings reveal the dynamic patterns of hair follicle development in Rex rabbits across phenotypic, histological, and molecular levels, providing a theoretical basis for the genetic regulation of fur quality.

Hair yield is the main economic value of Zhexi Angora rabbit, and it is an important index to measure its productive traits. The TRPV3 gene has been found to be associated with wool yield. This study aims to investigate the correlation between TRPV3 and wool production traits in rabbits, with the goal of improving wool yield. In the current study, flow cytometry and CCK-8 assays were used to investigate the effect of the TRPV3 gene on the proliferation and apoptosis of dermal papilla cells (DPCs) in rabbit hair follicles (HFs). Results showed that the TRPV3 gene regulates the mRNA expression of genes involved in HF development (BMP4, SFRP2, TGF-β1, WNT5a, and STAT1), as detected by qRT-PCR analysis. The core promoter region of TRPV3 was identified through dual luciferase activity tests, and Sanger sequencing was used to detect polymorphisms in both the exonic and promoter regions of TRPV3. The analysis showed a single SNP in the exon region, which had no significant association with wool production. However, five SNPs were detected in the promoter region, with the g.48897415G> A site showing a significant association with wool production in Zhexi Angora rabbits. Moreover, rabbits carrying the AA genotype also showed higher transcriptional activity. The mutation at g.48897415G> A in the promoter region introduced seven extra transcription factors (TFs) (RFX4, RFX3, RFX2, ZNF45, RFX1, Zfp668, and ZNF655). In conclusion, the g.48897415G > A mutation in TRPV3 is significantly associated with wool yield, and the TRPV3 gene inhibits the proliferation of DPCs. This locus can be used as a molecular marker for wool traits in rabbits, allowing early selection and precise breeding of high-wool-yield strains to shorten the breeding cycle and improve efficiency to enhance both the yield and quality of rabbit wool.

Rabbit meat is widely recognized for its favorable nutritional properties, while the molecular mechanisms underlying differences in meat quality between New Zealand White rabbits and Rex rabbits are essential for rabbit production. In this study, a total of 120 healthy 13-week-old rabbits (60 per group) were used to evaluate meat quality traits. The longissimus dorsi muscle (LDM) was then collected for transcriptomic and metabolomic analyses. The results showed that New Zealand White rabbits exhibited significantly higher live weight before slaughter, eviscerated weight, semi-eviscerated weight, and pH24 (p < 0.01), whereas Rex rabbits displayed higher cooking loss (p < 0.01) and intramuscular fat content (p < 0.05). Metabolomic profiling identified 218 differential metabolites (DMs), which were mainly enriched in amino acid biosynthesis and the pentose phosphate pathway, including key metabolites such as DL-arginine, gallic acid, and lipid-related compounds. Transcriptomic analysis identified 227 differentially expressed genes (DEGs) enriched in pathways associated with muscle development and meat quality, including oxidative phosphorylation, FoxO, and MAPK signaling pathways. Key DEGs, such as MYH13, HOXA13, and PDK4, were associated with muscle fiber formation and fat deposition. Integrated analysis revealed that 34 DEGs and 24 DMs were co-enriched in 26 pathways, with strong correlations observed between oxidative phosphorylation-related genes and energy metabolites, as well as between collagen-associated genes and amino acids. These findings establish a gene-metabolite regulatory network underlying breed-specific differences in meat quality and identify potential molecular markers to improve rabbit meat quality and to better understand muscle metabolism across different rabbit breeds.