1.Serpina3c Mitigates Adipose Tissue Inflammation by Inhibiting the HIF1α-Mediated Endoplasmic Reticulum Overoxidation in Adipocytes
Yu JIANG ; Jia-Qi GUO ; Ya WU ; Peng ZHENG ; Shao-Fan WANG ; Meng-Chen YANG ; Gen-Shan MA ; Yu-Yu YAO
Diabetes & Metabolism Journal 2026;50(1):62-76
Background:
Visceral white adipose tissue (vWAT) inflammation is a critical pathology of obesity-caused heart damage and is closely associated with adipocyte endoplasmic reticulum (ER) dysfunction. Serine (or cysteine) peptidase inhibitor, clade A, member 3C (Serpina3c) has been identified as an adipokine with anti-vWAT inflammatory effects. However, it remains unclear whether Serpina3c deficiency promotion of vWAT inflammation involves adipocyte ER dysfunction and whether it further contributes to heart damage in obesity.
Methods:
Wild type and Serpina3c knockout (Serpina3c–/–) mice were fed a high-fat diet (HFD) for 12 weeks. An adeno-associated virus (AAV) was injected locally into epididymal white adipose tissue (eWAT) of Serpina3c–/– mice to induce eWAT-adipocyte- specific overexpression of Serpina3c (AAV-Serpina3c) or knockdown of hypoxia-inducible factor 1α (AAV-shHIF1α). In vitro experiments were performed in 3T3-L1 adipocytes.
Results:
Serpina3c–/– mice exhibited more severe eWAT, serum and heart inflammation after HFD feeding. Consistently, these adverse phenotypes were mitigated in AAV-Serpina3c and AAV-shHIF1α mice. Mechanistically, ER oxidoreductase 1α (Ero1α) and protein disulfide isomerase (PDI) family members PDIA3 and PDIA4 were found to be target genes of HIF1α. In the obese mice, Serpina3c deficiency caused adipocyte more hypertrophy, and activated HIF1α-Ero1α/PDI mediated ER overoxidation and ER stress in eWAT. Subsequently, this led to increased adipocyte apoptosis and chemokine production and decreased adiponectin expression, which promoted macrophage infiltration and M1 polarization in eWAT, thus exacerbating eWAT inflammation and ultimately facilitating serum and distal heart inflammation.
Conclusion
These findings indicate that Serpina3c is a significant regulator of adipocyte ER redox homeostasis, thus highlighting Serpina3c as a potential therapeutic target for obesity-related eWAT inflammation and heart damage.
2.Immunodynamic changes in a mouse model of malignant pleural effusion
Xiao-Lei WEI ; Xu GUO ; Chuang-Xin ZHANG ; Qi WANG ; Xiao-Fan LIU ; Ming-Ming SHAO ; Huan-Zhong SHI ; Kan ZHAI
Laboratory Animal Research 2026;42(1):59-67
Background:
Malignant pleural effusion (MPE), a common complication of advanced cancers, is associated with poor prognosis and reduced quality of life. Although host–tumor interactions are known to drive MPE development, the associated immune dynamics during disease progression remain unclear. Using a Lewis lung carcinoma-induced MPE model in C57BL/6JNidfc mice, we systematically evaluated general parameters and immune cell changes at two-day intervals throughout disease progression.
Results:
The day of Lewis lung carcinoma cell injection into the pleural space was designated as day 0. By day 10 post-injection (p.i.), MPE-bearing mice exhibited ~ 10% body weight loss, marking the experimental endpoint. Pleural tumor mass and pleural effusion volume were minimal up to day 4 p.i. but increased sharply from day 6 onward.CD45⁺ immune cell counts rose over time, and days 6, 8, and 10 p.i. marked key stages of MPE progression. On day 6, B cells, T cells, and natural killer cells, but not macrophages and neutrophils, increased significantly compared to earlier timepoints. By day 8, all immune cell subsets except T cells exceeded day 6 levels, and at day 10, natural killer cell numbers declined while others continued to increase. Besides, the numbers of CD8⁺ T cells, Th1 cells, regulatory T cells, and M2 macrophages progressively increased from day 6 to 10. Based on these data, days 6 and 10 were defined as early and advanced MPE stages, respectively, with distinct immune phenotypes. In advanced MPE, CD8⁺ T cells displayed reduced IFN-γ, TNF-α, Granzyme B, Perforin, FasL, and Ki-67, but upregulated PD-1 and CTLA-4 relative to early stage. Similarly, Th1 cells showed decreased IFN-γ, TNF-α, and IL-2 production along with reduced Ki-67 expression. Advanced-stage M2 macrophages exhibited lower MHC-II levels and impaired phagocytosis, but higher PD-L1 and IL-10 production, while neutrophils showed reduced TNF-α release and phagocytic activity.
Conclusions
Our findings characterize the temporal immune dynamics associated with MPE progression in a mouse model, revealing a transition from an early immunostimulatory state to a late immunosuppressive state. This study enhances our understanding of MPE immunopathogenesis and provides a foundation for developing precise, stagespecific therapeutic strategies.
3.Effect of Aerobic Exercise Combined with Anmeidan on Learning Memory and Synaptic Plasticity in Rats with Sleep Deprivation Based on BDNF/TrkB/CREB Signaling Pathway
Yunyuan GUO ; Yuping SHAO ; Qiuchan ZENG ; Lixia LIN ; Guangjing XIE
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(17):117-124
ObjectiveThis paper aims to study the effects of four weeks of aerobic exercise combined with Anmeidan on the synaptic plasticity marker protein and synaptic ultrastructure of the hippocampus in the model rats with sleep deprivation, thereby investigating the possible mechanism of its action to improve the learning memory of rats with sleep deprivation. Methods50 Sprague-Dawley (SD) rats were randomly divided into blank control group (group C), sleep deprivation group (group M), aerobic exercise + sleep deprivation group (group MEX), Anmeidan + sleep deprivation group (group MA, 18.18 g∙kg-1∙d-1), and aerobic exercise + Anmeidan + sleep deprivation group (group MEXA, 18.18 g∙kg-1∙d-1). Anmeidan was administered by gavage in the MA group for four weeks. Aerobic exercise was performed in the MEX group for four weeks. Anmeidan was administered by gavage in the MEXA group in combination with aerobic exercise for four weeks, and sleep deprivation was performed for 72 h by using the multi-platform water environment method. At the end of sleep deprivation, Morris water maze was used to assess the learning and memory ability of rats in each group, and hematoxylin-eosin (HE) staining was used to observe the morphological changes of rats' hippocampal neurons. A transmission electron microscope was used to observe the synaptic ultrastructure of rats' hippocampus. The expression levels of brain-derived neurotrophic factor (BDNF), tyrosine kinase receptor B (TrkB), cAMP-response element binding protein (CREB), postsynaptic density-95 (PSD-95), and synaptophysin (SYN) were detected by Western blot, and the real-time fluorescence quantitative polymerase chain reaction (Real-time PCR) was used to detect the relative mRNA expression levels of BDNF, TrkB, and CREB in the rats' hippocampus. ResultsCompared with those in group C, rats in group M had significantly longer latency and total swimming distance on the platform (P<0.01) and a significantly reduced number of traversals across the platform as well as the residence time in the target quadrant (P<0.01). Part of the hippocampal neurons damaged, with a reduced number, disorganized arrangement, fuzzy synaptic gaps, thinning of post-synaptic dense material, and uneven density of synaptic vesicles. The protein expression levels and relative mRNA expression levels of BDNF, TrkB, and CREB were significantly reduced (P<0.01), and the protein expression levels of PSD-95 and SYN were significantly reduced (P<0.01). Compared with those in group M, rats in MA, MEX, and MEXA groups showed a decrease in latency to platform and total distance swum, an increase in the number of traversals across the platform and residence time in the target quadrant (P<0.05, P<0.01), a reduction in hippocampal neuronal damage, a better arrangement, a more intact synaptic structure, a thickening of post-synaptic dense material, a uniform density of synaptic vesicles, and an increase in the protein expression levels and mRNA expression levels of BDNF, TrkB, and CREB (P<0.05, P<0.01). The protein expressions of PSD-95 and SYN rose (P<0.05, P<0.01). ConclusionAerobic exercise combined with Anmeidan can improve learning memory in rats with sleep deprivation, and its mechanism of action may be related to the modulation of the BDNF/TrkB/CERB signalling pathway, up-regulation of the expression of PSD-95 and SYN, and improvement of synaptic structural damage. The combination of interventions is superior to single exercise or drugs.
4.The influence of mechanical pressure on the migration of dural cells in different parts and their ability to promote bone formation
Haidong ZHANG ; Jie SHEN ; Yajie GAO ; Guo SHAO ; Chunyang ZHANG ; Zhijun ZHAO
Acta Universitatis Medicinalis Anhui 2026;61(9):1576-1583
ObjectiveTo explore the effects of mechanical pressure regulation on the migration and bone-promoting ability of suture dural cells (S-DCs) and non-suture dural cells (NS-DCs). MethodsDural cells (S-DCs), non-cranial suture dural cells (NS-DCs) and cranial suture mesenchymal stem cells (CS-MSCs) of 5-day-old SD rats were isolated and cultured. Four experimental conditions, namely S-DCs-Normal, S-DCs-Stress, NS-DCs-Normal and NS-DCs-Stress, were set according to the source of the cells and whether mechanical pressure (1.07 kPa, 24 hours) was applied. The migration ability of dural cells was detected by cell scratch test. Four experimental condition culture media were collected and co-cultured with CS-MSCs for osteogenic induction. Calcium salt deposition was detected by alizarin red staining, and the expression of osteogenesis-related proteins was detected by Western blot. ResultsCompared with the Normal group, the migration abilities of both S-DCs and NS-DCs decreased after Stress treatment (P<0.05). Compared with S-DCs, NS-DCs has a weaker migration ability under the same processing conditions (P<0.05). The conditioned medium experiment showed that Stress treatment reduced the osteogenic ability of CS-MSCs (P<0.05), and the osteogenic effect of the conditioned medium derived from NS-DCs was weaker than that of S-DCs (P<0.05). The Western blot results were consistent with the trend of alizarin red staining. Both Stress treatment and NS-DCs sources could down-regulate the expression of osteogenesis-related proteins (P<0.05). ConclusionMechanical stress can significantly inhibit the migration of dural cells and the osteogenic differentiation process of CS-MSCs mediated by it. The mechanical tolerance and osteogenic regulation ability of S-DCs are significantly better than those of NS-DCs.
5.Bawei Chenxiang Wan Protects Against Acute Myocardial Ischemia by Activating Phosphatidylinositol 3-Kinase to Inhibit Cuproptosis in Rats
Xiaoying ZHANG ; Yuquan XIE ; Yuchan ZHANG ; Qi SI ; Yuanhu XIAO ; Yuqi GUO ; Xiayu SHAO
Journal of Sun Yat-sen University(Medical Sciences) 2026;47(5):820-832
ObjectiveTo investigate the protective effect and underlying mechanisms of the Bawei Chenxiang Wan (BCW) against myocardial ischemic injury. MethodsMyocardial ischemia in vivo was induced in rats by subcutaneous injection of isoproterenol (ISO), and ex vivo ischemia was established by coronary artery ligation in isolated rat hearts. The effects of BCW, alcohol extracts and its polar extracts were evaluated on ST segment on electrocardiogram (ECG), myocardial damage, hemodynamic parameters, and infarct size. The phosphorylation level of phosphatidylinositol 3-kinase (PI3K), the expression of cuproptosis-related proteins, and the content of Cu²⁺ in myocardial tissue were detected. The regulatory relationship of the signaling pathway was verified using an oxygen-glucose deprivation (OGD) myocardial cell injury model, combined with PI3K agonists and inhibitors. ResultsBCW ameliorated ST-segment elevation on electrocardiograms(P<0.01), reduced serum levels of myocardial injury markers, improved hemodynamic parameters, upregulated PI3K phosphorylation(P<0.01), and decreased Cu²⁺ accumulation in rats with myocardial ischemia(P<0.01). Moreover, BCW reduced the myocardial infarct size. In the isolated rat heart model of ischemia, both the ethanol extract and various solvent fractions of BCW exerted protective effects and reduced Cu²⁺ content, among which the n-butanol fraction exhibited the most potent activity(P<0.01). Specifically, the n-butanol fraction upregulated PI3K phosphorylation(P<0.01) and downregulated the expression of cuproptosis-related proteins, including ferredoxin reductase 1(FDX1)(P<0.05), lipoic acid synthetase(LIAS), and dihydrolipoamide S-acetyltransferase(DLAT) oligomerization(P<0.05). In the OGD-induced cardiomyocyte injury model, treatment with a PI3K agonist inhibited DLAT oligomerization(P<0.05), whereas co-administration of a PI3K inhibitor attenuated the inhibitory effect of the n-butanol fraction on DLAT oligomer formation(P<0.05). ConclusionThe n-butanol fraction of BCW exerts a significant protective effect against myocardial ischemic injury, and its mechanism may involve activation of the PI3K and inhibition of cuproptosis.
6.Bawei Chenxiang Wan Protects Against Acute Myocardial Ischemia by Activating Phosphatidylinositol 3-Kinase to Inhibit Cuproptosis in Rats
Xiaoying ZHANG ; Yuquan XIE ; Yuchan ZHANG ; Qi SI ; Yuanhu XIAO ; Yuqi GUO ; Xiayu SHAO
Journal of Sun Yat-sen University(Medical Sciences) 2026;47(5):820-832
ObjectiveTo investigate the protective effect and underlying mechanisms of the Bawei Chenxiang Wan (BCW) against myocardial ischemic injury. MethodsMyocardial ischemia in vivo was induced in rats by subcutaneous injection of isoproterenol (ISO), and ex vivo ischemia was established by coronary artery ligation in isolated rat hearts. The effects of BCW, alcohol extracts and its polar extracts were evaluated on ST segment on electrocardiogram (ECG), myocardial damage, hemodynamic parameters, and infarct size. The phosphorylation level of phosphatidylinositol 3-kinase (PI3K), the expression of cuproptosis-related proteins, and the content of Cu²⁺ in myocardial tissue were detected. The regulatory relationship of the signaling pathway was verified using an oxygen-glucose deprivation (OGD) myocardial cell injury model, combined with PI3K agonists and inhibitors. ResultsBCW ameliorated ST-segment elevation on electrocardiograms(P<0.01), reduced serum levels of myocardial injury markers, improved hemodynamic parameters, upregulated PI3K phosphorylation(P<0.01), and decreased Cu²⁺ accumulation in rats with myocardial ischemia(P<0.01). Moreover, BCW reduced the myocardial infarct size. In the isolated rat heart model of ischemia, both the ethanol extract and various solvent fractions of BCW exerted protective effects and reduced Cu²⁺ content, among which the n-butanol fraction exhibited the most potent activity(P<0.01). Specifically, the n-butanol fraction upregulated PI3K phosphorylation(P<0.01) and downregulated the expression of cuproptosis-related proteins, including ferredoxin reductase 1(FDX1)(P<0.05), lipoic acid synthetase(LIAS), and dihydrolipoamide S-acetyltransferase(DLAT) oligomerization(P<0.05). In the OGD-induced cardiomyocyte injury model, treatment with a PI3K agonist inhibited DLAT oligomerization(P<0.05), whereas co-administration of a PI3K inhibitor attenuated the inhibitory effect of the n-butanol fraction on DLAT oligomer formation(P<0.05). ConclusionThe n-butanol fraction of BCW exerts a significant protective effect against myocardial ischemic injury, and its mechanism may involve activation of the PI3K and inhibition of cuproptosis.
7.Molecular Mechanisms of LIGHT Regulating Tumor Vascular Microenvironment and Its Precision Delivery Strategies for Solid Tumor Immunotherapy
Jun-Yi YUAN ; Shao-Xia WANG ; Li-Ming JIN ; Bin-Chun LI ; Guo-Bin DING
Progress in Biochemistry and Biophysics 2026;53(10):2583-2595
The drug resistance in the treatment of solid tumors is closely related to abnormalities in the tumor vascular microenvironment (TVM). The TVM is dynamically composed of multiple stromal, vascular, and immune cell populations together with extracellular matrix. Its structural disorder and functional imbalance can lead to abnormal angiogenesis, perfusion disorders, limited drug delivery, and insufficient immune cell infiltration, thereby creating a microenvironment conducive to tumor progression and treatment resistance. Therefore, the coordinated regulation of TVM through vascular normalization and immune remodeling has become an important research direction for improving the treatment effect of solid tumors. Tumor necrosis factor superfamily member 14 (TNFSF14), also known as LIGHT (homologous to lymphotoxin, inducible, competes with herpes simplex virus (HSV) glycoprotein D for herpesvirus entry mediator (HVEM), expressed by T lymphocyte), is an important molecule connecting tumor vascular remodeling and immune regulation. LIGHT can bind to the lymphotoxin β receptor (LTβR) to activate the NF-κB (nuclear factor kappa B)-related signaling pathway, regulate the functions of vascular endothelial cells and stromal cells, and induce the expression of adhesion molecules and chemokines such as VCAM-1(vascular cell adhesion molecule 1), ICAM-1(intercellular adhesion molecule 1), CCL19 (C-C motif chemokine ligand 19), CCL21 (C-C motif chemokine ligand 21), and CXCL13 (C-X-C motif chemokine ligand 13), promoting the formation of high endothelial venules (HEVs). HEVs can improve the vascular access of immune cells into tumor tissues and further promote the formation of tertiary lymphoid structures (TLS), providing a structural basis for the recruitment of effector T cells and sustained anti-tumor immune responses. At the same time, LIGHT interacts with HVEM to provide costimulatory signals to T cells, enhancing their activation, proliferation, and cytotoxic function. Thus, LIGHT can link tumor vascular normalization, immune cell recruitment, and T cell activation through the dual actions mediated by LTβR and HVEM, forming a coordinated regulation model of “vascular remodeling-immune infiltration-immune activation”, providing new molecular targets for the treatment of solid tumors. Despite LIGHT’s good anti-tumor potential, its therapeutic application is still limited by factors such as insufficient stability in vivo, short half-life, and potential off-target effects due to systemic exposure. In recent years, researchers have developed various strategies for the precise delivery of LIGHT, including fusion proteins, bacterial vectors, viral vectors, nanoparticles, chimeric antigen receptor T cells (CAR-T), and mesenchymal stem cells (MSCs), to enhance the enrichment, expression, or sustained release of LIGHT in tumor sites through different approaches, thereby improving its therapeutic efficacy and safety. This article systematically reviews the structural characteristics, biological functions, and molecular mechanisms mediating TVM remodeling by LIGHT, with a focus on the signal transduction mediated by LTβR and HVEM and their roles in tumor immune regulation. Subsequently, it systematically outlines the molecular mechanisms by which LIGHT regulates the tumor vascular microenvironment and its intrinsic connection with immune cell recruitment and activation, from the perspectives of TVM abnormalities, vascular normalization, HEV formation, and TLS induction. Furthermore, it categorizes and summarizes precise delivery strategies such as LIGHT fusion proteins, bacterial vectors, viral vectors, nanoparticles, CAR-T cells, and MSCs according to delivery vectors and modes of action, and compares their functional characteristics, antitumor effects, and potential advantages and limitations. On this basis, the article further discusses the key issues that LIGHT therapeutic strategies still face in terms of targeting, controllability,in vivo stability, safety, and clinical translation, and anticipates the potential value of its combination with immune checkpoint inhibitors, anti-angiogenic therapy, and other tumor treatment methods. This article aims to deepen the understanding of the antitumor mechanism of LIGHT from the perspective of synergistic regulation of tumor vascular microenvironment remodeling and immune activation, providing theoretical basis and new research ideas for the design of solid tumor treatment strategies based on precise regulation of TVM and the clinical translation of LIGHT-related treatment systems.
8.Phenomics of traditional Chinese medicine 2.0: the integration with digital medicine
Min Xu ; Xinyi Shao ; Donggeng Guo ; Xiaojing Yan ; Lei Wang ; Tao Yang ; Hao LIANG ; Qinghua PENG ; Lingyu Linda Ye ; Haibo Cheng ; Dayue Darrel Duan
Digital Chinese Medicine 2025;8(3):282-299
Abstract
Modern western medicine typically focuses on treating specific symptoms or diseases, and traditional Chinese medicine (TCM) emphasizes the interconnections of the body’s various systems under external environment and takes a holistic approach to preventing and treating diseases. Phenomics was initially introduced to the field of TCM in 2008 as a new discipline that studies the laws of integrated and dynamic changes of human clinical phenomes under the scope of the theories and practices of TCM based on phenomics. While TCM Phenomics 1.0 has initially established a clinical phenomic system centered on Zhenghou (a TCM definition of clinical phenome), bottlenecks remain in data standardization, mechanistic interpretation, and precision intervention. Here, we systematically elaborates on the theoretical foundations, technical pathways, and future challenges of integrating digital medicine with TCM phenomics under the framework of “TCM phenomics 2.0”, which is supported by digital medicine technologies such as artificial intelligence, wearable devices, medical digital twins, and multi-omics integration. This framework aims to construct a closed-loop system of “Zhenghou–Phenome–Mechanism–Intervention” and to enable the digitization, standardization, and precision of disease diagnosis and treatment. The integration of digital medicine and TCM phenomics not only promotes the modernization and scientific transformation of TCM theory and practice but also offers new paradigms for precision medicine. In practice, digital tools facilitate multi-source clinical data acquisition and standardization, while AI and big data algorithms help reveal the correlations between clinical Zhenghou phenomes and molecular mechanisms, thereby improving scientific rigor in diagnosis, efficacy evaluation, and personalized intervention. Nevertheless, challenges persist, including data quality and standardization issues, shortage of interdisciplinary talents, and insufficiency of ethical and legal regulations. Future development requires establishing national data-sharing platforms, strengthening international collaboration, fostering interdisciplinary professionals, and improving ethical and legal frameworks. Ultimately, this approach seeks to build a new disease identification and classification system centered on phenomes and to achieve the inheritance, innovation, and modernization of TCM diagnostic and therapeutic patterns.
9.Role of TIM3 Pathway in Immune Pathogenesis and Targeted Therapy of Myelodysplastic Syndrome
Xinyu GUO ; Shunjie YU ; Jinglian TAO ; Yingshuai WANG ; Xiaotong REN ; Zhaoyun LIU ; Rong FU ; Zonghong SHAO ; Lijuan LI
Cancer Research on Prevention and Treatment 2025;52(9):731-735
Myelodysplastic syndrome (MDS), a myeloid tumor derived from the malignant clones of hematopoietic stem cells, has an annually increasing incidence. The contemporary research direction has shifted to analyzing the synergistic effect of immune surveillance collapse and abnormal bone marrow microenvironment in the pathological process of MDS. Against this backdrop, the immune checkpoint molecule TIM3 has emerged as a key target because of its persistently high expression on the surface of important immune cells such as T and NK cells. The abnormal activation of the TIM3 pathway is the mechanism by which solid tumors and hematological malignancies achieve immune escape and is a key hub in the formation of immune exhaustion phenotypes. This work integrates the original discoveries of our team with the latest international progress, systematically demonstrating the bidirectional regulatory network of TIM3 between the malignant clone proliferation of MDS and the immunosuppressive microenvironment. Integrating the evidence from emerging clinical trials allows us to consider the clinical significance of TIM3-targeted blocking for MDS, providing a transformative path to overcome the resistance of traditional treatments and marking a new chapter in the active immune reconstitution of MDS treatment.
10.Molecular Mapping and Functional Analysis of Phenotype-determining Genes for Mendelian Traits in Pea
Progress in Biochemistry and Biophysics 2025;52(10):2447-2461
Mendel established the laws and laid the foundation of modern genetics through his famous hybridization experiments on seven pairs of classic traits in the garden pea (Pisum sativum). However, the molecular bases underlying these traits have only come into sharp focus in recent years. Leveraging advances in traditional map-based cloning, TILLING, long-read resequencing, population genetics, and GWAS, this article synthesizes current knowledge of ten genes governing seven traits—plant height, seed shape, flower color, seed color, pod color, pod morphology, and flower position—by summarizing each gene’s identity, chromosomal localization, and functional pathway. For plant height, the classical Le locus corresponds to PsGA3ox1, which encodes a gibberellin 3β-hydroxylase. Mutations at Le impede the biosynthesis of the bioactive hormone GA1, and the resulting deficiency leads to a dwarf or reduced-stature phenotype. Seed shape is determined by R, identified as PsSBEI (starch-branching enzyme I). Insertion of a transposable element into R restricts amylopectin synthesis, perturbing endosperm starch architecture and resulting in the wrinkled seeds noted by Mendel. Flower color is specified by the coordinated action of A (a bHLH transcription factor) and A2 (a WD40 scaffold). Together, they assemble the canonical MYB-bHLH-WD40 (MBW) regulatory complex, which co-activates structural genes in the anthocyanin pathway to determine pigment accumulation and floral hue. Seed color is governed by I, which encodes PsSGR (STAY-GREEN), a magnesium dechelatase that catalyzes a key step in chlorophyll catabolism. Loss-of-function alleles at I block chlorophyll degradation, yielding “stay-green” seeds in which chlorophyll persists beyond normal developmental stages. Pod coloration maps to Gp, corresponding to ChlG (chlorophyll synthase). Either direct loss of ChlG function or readthrough-fusion transcriptional interference caused by a large upstream deletion suppresses chlorophyll biosynthesis in developing pods, resulting in the yellow-pod phenotype. Pod morphology depends on two convergent regulatory pathways. The P gene, PsCLE41, signals through the P-PXY-WOX/NAC axis to promote vascular differentiation and secondary-wall programs, while V encodes PsMYB26, a transcription factor that drives secondary wall thickening in fiber cells. Acting in concert, these modules ensure robust secondary-wall deposition in the fiber layer lining the inner pod wall; disruption of either component compromises wall thickening and leads to pleated or wrinkled pods. Flower position (inflorescence determinacy at the shoot apex) is controlled by FA, identified as PsCIK, which participates in the CLAVATA-WUSCHEL (CLV-WUS) feedback circuit that maintains shoot apical meristem homeostasis. Mutations in FA destabilize this self-regulatory loop and promote terminal flowers at the apex. The expressivity of this determinacy phenotype is further modulated by a recessive modifier, Mfa, which fine-tunes the outcome in the fa background. Across these loci, convergent evidence highlights the central role of structural variation in generating the classical Mendelian phenotypes. Building on this clarified molecular landscape, we outline practical implications for quality improvement and the deliberate “design” of traits. Looking ahead, we envisage a next generation of legume genetic improvement anchored on three mutually reinforcing pillars: high-quality reference genomes to deliver contiguous, structurally faithful assemblies; comprehensive pan-genomes to capture presence/absence variation and structural polymorphism across germplasm; and precise gene editing to target coding, regulatory, and structural features alike. Together, these tools chart a path toward mechanism-based breeding, enabling purposeful, design-driven trait improvement in peas and, by extension, other legumes.

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