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22 pages, 10841 KB  
Article
Visceral Peritoneum Hyperpigmentation in Chickens Is Associated with DCT Expression
by Xu Dong, Qingchun Liu, Jiabao Xing, Guodong Mo, Muyang Li, Qinghua Nie, Jingting Shu and Zhenhui Li
Animals 2025, 15(21), 3076; https://doi.org/10.3390/ani15213076 (registering DOI) - 23 Oct 2025
Abstract
Hyperpigmentation of the visceral peritoneum (HVP) is a pigmentation abnormality in chickens that adversely affects carcass appearance, consumer acceptance, and poultry production. However, the genetic basis of HVP remains unclear. To investigate the causes and regulatory mechanisms of HVP, we employed high-performance liquid [...] Read more.
Hyperpigmentation of the visceral peritoneum (HVP) is a pigmentation abnormality in chickens that adversely affects carcass appearance, consumer acceptance, and poultry production. However, the genetic basis of HVP remains unclear. To investigate the causes and regulatory mechanisms of HVP, we employed high-performance liquid chromatography (HPLC), bulk RNA sequencing (RNA-seq), qRT-PCR, Western blotting, and siRNA interference. Additionally, single-cell RNA sequencing (scRNA-seq) was used to examine gene expression at the cellular level. Anatomical examination and hematoxylin and eosin (HE) staining revealed melanin deposition in the peritoneum of HVP-affected chickens. Spectrophotometric analysis at 500 nm showed significantly higher absorbance in the HVP group (p < 0.05), which correlated with the degree of pigmentation. HPLC confirmed the pigmentation as eumelanin, based on the pyrrole-2,3,5-tricarboxylic acid (PTCA) peak. RNA-seq identified 61 differentially expressed genes. Functional studies showed that dopachrome tautomerase (DCT) overexpression, combined with L-tyrosine (L-Tyr) supplementation, significantly increased melanin content (p < 0.05) and promoted melanocyte proliferation. In contrast, DCT silencing reduced melanin secretion and inhibited cell growth. ScRNA-seq analysis of over 9700 high-quality cells identified distinct melanocyte clusters, with DCT expression approximately 2.5-fold higher in melanocytes from the HVP group compared to the normal group. Furthermore, a DCT polymorphism (g.147917398 C > T) was identified as a potential marker for genetic selection (p-values = 0.033). These findings demonstrate that HVP is driven by DCT overexpression and excessive eumelanin deposition. DCT could serve as a molecular marker for genomic selection to improve poultry carcass quality and reduce economic losses in the poultry industry. Full article
(This article belongs to the Special Issue Genetic Diversity and Conservation of Local Poultry Breeds)
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18 pages, 4385 KB  
Article
Transcriptomic Analysis of Anthocyanin Degradation in Salix alba Bark: Insights into Seasonal Adaptation and Forestry Applications
by Hong-Yong Wang, Xing-Ju Liu, Meng-Zhen Yin, Sheng-Jia Cui, Hai-Yong Liang and Zhen-Hua Xu
Forests 2025, 16(10), 1598; https://doi.org/10.3390/f16101598 - 17 Oct 2025
Viewed by 192
Abstract
Anthocyanins, key flavonoid-derived secondary metabolites, not only confer diverse pigmentation but also function in photoprotection, antioxidative defense, and cold acclimation. In woody species, bark anthocyanin turnover is tightly linked to environmental adaptation, stress resilience, and ornamental traits, yet its molecular regulation remains largely [...] Read more.
Anthocyanins, key flavonoid-derived secondary metabolites, not only confer diverse pigmentation but also function in photoprotection, antioxidative defense, and cold acclimation. In woody species, bark anthocyanin turnover is tightly linked to environmental adaptation, stress resilience, and ornamental traits, yet its molecular regulation remains largely unresolved. Here, we investigated Salix alba L. bark by integrating anthocyanin quantification, transcriptome profiling, and weighted gene co-expression network analysis (WGCNA) to dissect the temporal dynamics and regulatory architecture of anthocyanin degradation. Anthocyanin content peaked at D2 (late December 2024), declined through D3 (mid-January 2025) and D4 (mid-February 2025), and partially rebounded at D5 (early March 2025), coinciding with peak expression of structural genes LAC1/2, POD1/2, and BGLU10. These enzymes co-expressed with multiple transcription factors, including MYB, bHLH, and WRKY families, forming putative core modules. Functional enrichment indicated that differentially expressed genes were enriched in redox processes, glycoside hydrolysis, flavonoid metabolism, and hormone signaling, suggesting a degradation mechanism mediated by reactive oxygen species, glycosidic cleavage, and hormone–transcription factor interplay. This study provides the first comprehensive framework of bark anthocyanin degradation in white willow, advancing the understanding of pigment dynamics, gene–environment crosstalk, and breeding strategies for ornamental woody plants. Full article
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22 pages, 4420 KB  
Article
Seed Nanopriming Improves Jalapeño Pepper Seedling Quality for Transplantation
by Erick H. Ochoa-Chaparro, Juan J. Patiño-Cruz, Julio C. Anchondo-Páez, Alan Alvarez-Monge, Cristina L. Franco-Lagos and Esteban Sánchez
Seeds 2025, 4(3), 47; https://doi.org/10.3390/seeds4030047 - 22 Sep 2025
Viewed by 382
Abstract
Nanopriming with metal nanoparticles (NPs) is a promising strategy for improving seedling quality in horticultural crops. This study evaluated the effects of hydropriming, ZnO, SiO2, ZnO + SiO2, a ZnMo nanofertilizer, and two commercial biostimulants (Osmoplant and Codasil) on [...] Read more.
Nanopriming with metal nanoparticles (NPs) is a promising strategy for improving seedling quality in horticultural crops. This study evaluated the effects of hydropriming, ZnO, SiO2, ZnO + SiO2, a ZnMo nanofertilizer, and two commercial biostimulants (Osmoplant and Codasil) on the early development of Capsicum annuum L. seedlings. Morphological, physiological, and biochemical traits, including biomass, stem architecture, number of leaves, chlorophylls, carotenoids, SPAD index, and nitrate reductase (NR) activity, were measured under controlled conditions. The ZnO and ZnO + SiO2 treatments promoted stronger root growth, higher pigment content, and higher NR activity. SiO2 alone and ZnMo showed intermediate improvements, while Osmoplant and Codasil had more limited effects. Multivariate analyses provided complementary information: heat maps revealed correlations between traits, PCA differentiated treatment responses, and radar charts integrated performance profiles. Overall, the results provide promising evidence that seed nanopriming, particularly with ZnO and ZnO + SiO2, improves seedling vigor and transplant potential in jalapeño peppers. Full article
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23 pages, 4908 KB  
Article
Transcriptome Analysis and Physiological Response to Salinity Stress in Adzuki Bean (Vigna angularis) at the Seedling Stage
by Baomei Wu, Ying Zhang, Qiang Zhang, Linlin Hao, Yanru Guo, Min Xu, Weizhong Liu and Binbin Wang
Plants 2025, 14(17), 2722; https://doi.org/10.3390/plants14172722 - 1 Sep 2025
Viewed by 635
Abstract
Adzuki bean (Vigna angularis (Willd.) Ohwi & H. Ohashi) is a significant crop for its applications in both traditional medicine and nutritional diets in China. However, there remains a paucity of exploration employing an RNA-seq approach to investigate the molecular response mechanisms [...] Read more.
Adzuki bean (Vigna angularis (Willd.) Ohwi & H. Ohashi) is a significant crop for its applications in both traditional medicine and nutritional diets in China. However, there remains a paucity of exploration employing an RNA-seq approach to investigate the molecular response mechanisms of the species under salinity stress. In this study, Jin Xiao Dou 6 (JXD6) adzuki bean cultivar was subjected to 0 mmol/L (CK), 32.5 mmol/L, and 65.0 mmol/L NaCl treatments to preliminarily characterize salinity-induced alterations in plant height, chloroplast pigment contents, leaf surface humidity and temperature, H2O2 and O2 accumulation, activities of antioxidative enzymes, and transcriptome profiles. Under increasing NaCl concentrations, the plant height of JXD6 seedlings was progressively inhibited. Conversely, the unifoliate leaves exhibited elevated leaf surface temperature, increased contents of chlorophyll a, total chlorophyll and carotenoids, enhanced accumulation of O2, as well as heightened activities of superoxide dismutase, peroxidase, and catalase. Transcriptome profile analyses suggested that a total of 363 and 858 differentially expressed genes were obtained in the unifoliate leaves of adzuki bean seedlings treated with 32.5 mmol/L and 65.0 mmol/L NaCl groups, respectively. The up-regulated genes were mainly enriched in the spliceosome pathway, while the down-regulated genes were mainly enriched in pathways of plant hormone signal transduction, plant–pathogen interaction, and the MAPK signaling pathway in plants. These results provide new insight into exploring the response mechanisms of adzuki beans to salinity stress via transcriptome analyses. Full article
(This article belongs to the Section Plant Response to Abiotic Stress and Climate Change)
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16 pages, 2821 KB  
Article
Transcriptomic Analysis Reveals the Regulation Function of Calcium Ions Regarding Anthocyanin Biosynthesis in Lonicera japonica Under Cold Stress
by Jie Chen, Wenxi Zheng, Ruonan Que, Junle Lv, Pei Wang, Jiachen Li, Lin Zhang and Bingxian Yang
Horticulturae 2025, 11(9), 1023; https://doi.org/10.3390/horticulturae11091023 - 1 Sep 2025
Viewed by 533
Abstract
Lonicera japonica is a widely utilized medicinal and ornamental plant. Its secondary metabolism is highly sensitive to cold stress. Previous studies have demonstrated how L. japonica accumulates anthocyanin in response to cold stress, with calcium ions playing a potential role in the regulation. [...] Read more.
Lonicera japonica is a widely utilized medicinal and ornamental plant. Its secondary metabolism is highly sensitive to cold stress. Previous studies have demonstrated how L. japonica accumulates anthocyanin in response to cold stress, with calcium ions playing a potential role in the regulation. To further clarify the regulatory function of calcium ions regarding pigment formation under cold stress, transcriptomic analysis was conducted on exogenous calcium ions and calcium chelator EGTA-treated L. japonica under cold stress. The CaCl2 treatment markedly delayed changes in the pigmentation, and the plant maintained a higher chlorophyll content, whereas EGTA treatment enhanced anthocyanin accumulation and induced earlier and more intense leaf coloration. A total of 17,296 differentially expressed genes were co-expressed during cold stress, and calcium-responsive genes were predominantly enriched in phenylpropanoid biosynthesis, hormone signaling, and stress response pathways. Notably, key transcription factors such as MYBS3 and BRH1 were identified with expression patterns that closely correlated with pigment changes and stress adaptation. These results indicate the deep involvement of molecular mechanisms of calcium signaling in modulating pigment accumulation in response to cold stress, providing a theoretical foundation for improving both the ornamental and medicinal value of L. japonica under adverse environmental conditions. Full article
(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))
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34 pages, 9495 KB  
Article
Specific Assay Protocols for Porcine Single-Eye Retinal Pigment Epithelium Concerning Oxidative Stress and Inflammation
by Philipp Dörschmann, Marie Prinz, Greta Schmitkall, Johann Roider and Alexa Klettner
Int. J. Mol. Sci. 2025, 26(17), 8434; https://doi.org/10.3390/ijms26178434 - 29 Aug 2025
Viewed by 612
Abstract
The retinal pigment epithelium (RPE) is strongly involved in the pathogenesis of several retinal diseases, such as age-related macular degeneration (AMD). RPE models addressing specific pathological pathways are of high importance for understanding cellular pathomechanisms and pre-clinical screening of potential new therapeutics. The [...] Read more.
The retinal pigment epithelium (RPE) is strongly involved in the pathogenesis of several retinal diseases, such as age-related macular degeneration (AMD). RPE models addressing specific pathological pathways are of high importance for understanding cellular pathomechanisms and pre-clinical screening of potential new therapeutics. The goal of this study is to establish standard operation protocols for single-eye porcine RPE preparation for AMD-relevant models of oxidative stress (RPE-Ox) and inflammation (RPE-Inf). Porcine primary RPE were prepared from one eye and seeded into one well of 12-well plates or, for polar differentiation, in transwell inserts. Different coatings (Poly-ᴅ-Lysine and laminin) and serum content of media (10%, 5%, and 1%) were tested to determine optimal culture parameters. For RPE-Ox, cells were treated with NaIO3, CoCl2, or erastin; cell viability (thiazolyl blue tetrazolium bromide, MTT), and gene expression (RT-qPCR) were determined. For RPE-Inf, cells were treated with lipopolysaccharide (LPS), polyinosinic/polycytidylic acid (Poly I:C), or tumor necrosis factor alpha (TNF-α); cell viability (MTT), cytokine secretion (ELISA), and gene expression (RT-qPCR) were determined. For transwell plates in RPE-Inf, cell viability (MTT), polar cytokine secretion (ELISA), gene expression (RT-qPCR), and transepithelial electrical resistance (TEER) for barrier assessment were conducted. For RPE-Ox, effective LD50 could be achieved by using 24 h stimulation with 25 µm erastin, seven days after preparation in 5% serum cultures, without coating. For gene expression assessment, the use of Poly-ᴅ-Lysine is recommended. For RPE-Inf, three days of LPS stimulation (1 µg/mL) showed effective cytokine activation with 5% serum on uncoated 12-well plates. Transwell plates are not recommended for cytokine secretion assessment. It can be used for cell barrier assays in which LPS also showed effective cell barrier decrease and gene expression assays. Two specific best practice protocols for the use of porcine single-eye cultures in AMD research concerning oxidative stress and inflammation with optimized parameters were established and are provided. Full article
(This article belongs to the Special Issue Molecular Mechanisms and Treatment of Retinal Diseases)
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18 pages, 10425 KB  
Article
Synergistic Response Mechanism and Gene Regulatory Network of Arundo donax Leaf Under Multiple Stresses
by Yixin Huangfu, Yibo Sun, Weiwei Chen, Gongyao Shi, Baoming Tian, Gangqiang Cao, Luyue Zhang, Jialin Guo, Fang Wei and Zhengqing Xie
Horticulturae 2025, 11(8), 985; https://doi.org/10.3390/horticulturae11080985 - 19 Aug 2025
Viewed by 497
Abstract
Arundo donax exhibits strong comprehensive stress resistance and high levels of crude protein and crude fiber, making it an ideal perennial forage crop. It adapts to various abiotic stresses and serves as a new model for studying plant stress response mechanisms. A. donax [...] Read more.
Arundo donax exhibits strong comprehensive stress resistance and high levels of crude protein and crude fiber, making it an ideal perennial forage crop. It adapts to various abiotic stresses and serves as a new model for studying plant stress response mechanisms. A. donax frequently encounters diverse environmental stresses during agricultural production, including drought, waterlogging, and temperature extremes. However, the response mechanisms of A. donax to multiple stresses remains elusive. By analyzing publicly available transcriptome data, we identified 9089, 19,272, and 8585 differentially expressed genes (DEGs) and 742 DEGs shared in the leaves of A. donax under drought, waterlogging, and cold conditions. The data showed that A. donax exhibits differential activation patterns in endogenous hormone signaling (jasmonate/gibberellin), energy metabolism (UDP-glucosyltransferase), and nitrogen metabolism pathways (acyltransferase) under these stresses. DEGs involved in the nitrogen metabolism and phenylpropanoid metabolism pathways were significantly enriched, while the gene expression patterns of these pathways varied among the drought, waterlogging, and cold stress conditions. Different stresses could affect the nitrogen accumulation in A. donax leaves. In addition, pairwise DEG comparisons indicated active roles of antioxidant defense and photosynthetic system in multiple stress responses. Physiological measurements validated these transcriptional changes: the activities of antioxidant enzymes (catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD)) increased significantly, minimizing oxidative damage. Meanwhile, the photosynthetic pigments content also decreased in response to the three stresses. Soluble sugars, pyruvate, malate, and citrate, which are involved in energy metabolism in the leaves of A. donax, accumulated to sustain themaintenance of the plant’s own energy metabolism. In conclusion, our study revealed the transcriptome-based regulatory network related with synergistic response mechanisms of A. donax leaves under multiple stress conditions. Full article
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12 pages, 560 KB  
Article
Determination of Antioxidant Activity and Proximate Composition of a Variety of Red Pigmented Zea mays L. from Puebla, Mexico
by Jesabel Pineda-Quiroz, Juan Alex Hernández-Rivera, Ivonne Pérez-Xochipa, Pedro Antonio-López and Alan Carrasco-Carballo
AppliedChem 2025, 5(3), 18; https://doi.org/10.3390/appliedchem5030018 - 6 Aug 2025
Viewed by 769
Abstract
Corn is one of the most consumed cereals in the Mexican diet. In this country, there are multiple varieties that exhibit nutraceutical potential due to their content of different metabolites with biological activity, such as blue corn. Another variety that has received little [...] Read more.
Corn is one of the most consumed cereals in the Mexican diet. In this country, there are multiple varieties that exhibit nutraceutical potential due to their content of different metabolites with biological activity, such as blue corn. Another variety that has received little study is the red pigmented corn variety Chilac from Puebla, Mexico, which is being studied for its nutraceutical potential. A differential extraction using the Soxhlet method was carried out to evaluate the phenolic content, total flavonoid content, and monomeric anthocyanins, and free radical scavenging test was performed using the DPPH reagent. A proximate analysis was also conducted to identify the main macronutrients. The results of the proximate analysis were comparable to those of other traditional corn varieties, with carbohydrates being the macronutrient present in the highest amount at 77.9%. Regarding phenolic content and the presence of anthocyanins, the best extractions were obtained using alcoholic solvents; for example, ethanol for phenols, yielding 1368.420 ± 104.094 mg of gallic acid equivalents (GAE)/kg plant. In contrast, the flavonoid content was higher in the aqueous extract, with 833.984 ± 65.218 mg QE/Kg. In the case of the DPPH assay, the best result was obtained with ethyl acetate (73.81 ± 5.31%). These findings provide a foundation for expanding the use of corn varieties with nutraceutical potential, opening the possibility of studies focused on deeper characterization. Full article
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22 pages, 2242 KB  
Article
Quercetin Can Alleviate ETECK88-Induced Oxidative Stress in Weaned Piglets by Inhibiting Quorum-Sensing Signal Molecule Autoinducer-2 Production in the Cecum
by Hailiang Wang, Min Yao, Dan Wang, Mingyang Geng, Shanshan Nan, Xiangjian Peng, Yuyang Xue, Wenju Zhang and Cunxi Nie
Antioxidants 2025, 14(7), 852; https://doi.org/10.3390/antiox14070852 - 11 Jul 2025
Cited by 1 | Viewed by 831
Abstract
This study evaluated the inhibitory activity of quercetin at sub-inhibitory concentrations on quorum-sensing (QS) molecules in vitro and the effects of dietary supplementation with quercetin (for 24 consecutive days) on enterotoxigenic Escherichia coli (ETEC)-induced inflammatory and oxidative stress responses in weaned piglets. The [...] Read more.
This study evaluated the inhibitory activity of quercetin at sub-inhibitory concentrations on quorum-sensing (QS) molecules in vitro and the effects of dietary supplementation with quercetin (for 24 consecutive days) on enterotoxigenic Escherichia coli (ETEC)-induced inflammatory and oxidative stress responses in weaned piglets. The piglets were fed one of three diets: the basal diet (Con), ETEC challenge (K88) after the basal diet, or ETEC challenge (quercetin + K88) after the basal diet supplemented with 0.2% quercetin. In vitro experiments revealed that 5 mg/mL quercetin exhibited the strongest QS inhibitory activity and reduced pigment production by Chromobacterium violaceum ATCC12472 by 67.70%. In vivo experiments revealed that quercetin + K88 significantly increased immunoglobulin A (IgA), immunoglobulin M (IgM), and immunoglobulin G (IgG) levels in the serum, ileum mucosa, and colon mucosa; increased glutathione peroxidase (GSH-Px), catalase (CAT), and superoxide dismutase (SOD) levels in the serum, liver, and colon mucosa; and decreased cluster of differentiation 3 (CD3) and cluster of differentiation 8 (CD8)activity in the serum compared with K88 alone. Quercetin + K88 significantly alleviated pathological damage to the liver and spleen and upregulated antioxidant genes (nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1(HO-1), CAT, SOD, and glutathione s-transferase (GST)). Inducible nitric oxide synthase (iNOS) and kelch-like ech-associated protein 1 (Keap1), which cause oxidative damage to the liver and spleen, were significantly downregulated. The acetic acid content in the cecum was significantly increased, and the E. coli count and QS signal molecule autoinducer-2 (AI-2) yield were significantly reduced. In conclusion, 0.2% dietary quercetin can alleviate ETEC-induced inflammation and oxidative stress in weaned piglets. Full article
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19 pages, 2605 KB  
Article
Transcriptome and Metabolome Analyses of Flavonoid Biosynthesis During Berry Development of Muscadine Grape (Vitis rotundifolia Michx)
by Qiaofeng Yang, Changlin Li, Yan Wang, Xian Pei, Aixin Wang, Li Jin and Linchuan Fang
Plants 2025, 14(13), 2025; https://doi.org/10.3390/plants14132025 - 2 Jul 2025
Viewed by 671
Abstract
Flavonoids play a crucial role in plant development, resistance, and the pigmentation of fruits and flowers. This study aimed to uncover the mechanism of flavonoid biosynthesis and fruit coloring in muscadine grapes. Two muscadine genotypes (Paulk and Supreme) were investigated via metabolomic and [...] Read more.
Flavonoids play a crucial role in plant development, resistance, and the pigmentation of fruits and flowers. This study aimed to uncover the mechanism of flavonoid biosynthesis and fruit coloring in muscadine grapes. Two muscadine genotypes (Paulk and Supreme) were investigated via metabolomic and transcriptomic analysis during three developmental stages (bunch closure, veraison stage, and ripening stage). A total of 314 flavonoids were identified, with flavones and flavonols being the primary constituents. The contents of many differentially accumulated metabolites (DAMs) were higher at the veraison stage. The total anthocyanin content was upregulated during berry development, with the dominant type of anthocyanidin-3,5-O-diglucoside. Proanthocyanins accumulated higher levels in the ripening stage of Paulk than Supreme. Transcriptomic analyses revealed that over 46% of the DEGs exhibited higher expression levels in the bunch closure stage. Moreover, phenylalanine ammonia-lyase (PAL), cinnamyl 4-hydroxylase (C4H), and coumaryl CoA ligase (4CL) genes were upregulated during berry development, suggesting they promote second metabolites biosynthesis. The upregulation of dihydroflavonol 4-reductase (DFR) and leucoanthocyanin reductase (LAR) may related to the higher levels of PA in Paulk. Anthocyanidin synthase (ANS) and UDP-glucose:flavonoid-3-O-glucosyltransferase (UFGT) showed higher expression levels in the ripening stage, which may relate to the accumulation of anthocyanidins. This study provides comprehensive insights into flavonoid metabolism and berry coloration in Vitis rotundifolia. Full article
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21 pages, 7526 KB  
Article
Integrated Metabolome and Transcriptome Analysis Reveals the Mechanism of Anthocyanin Biosynthesis in Pisum sativum L. with Different Pod Colors
by Weijun Ye, Zejiang Wu, Dongfeng Tian and Bin Zhou
Agronomy 2025, 15(7), 1609; https://doi.org/10.3390/agronomy15071609 - 30 Jun 2025
Viewed by 762
Abstract
Pea (Pisum sativum L.) is a significant source of dietary protein, starch, fiber, and minerals, offering health benefits and serving as both a green vegetable and dry grain. The pigment contents in pea pods with different colors and related genes are still [...] Read more.
Pea (Pisum sativum L.) is a significant source of dietary protein, starch, fiber, and minerals, offering health benefits and serving as both a green vegetable and dry grain. The pigment contents in pea pods with different colors and related genes are still unclear. We conducted an integrated transcriptome and metabolome analysis on three cultivars, including QiZhen (QZ) with green immature pods, FengMi (FM) with yellow immature pods, and ZiYu (ZY) with purple immature pods, to identify the key genes and metabolites involved in anthocyanin accumulation. ZY showed the highest total anthocyanin content compared with FM and QZ. Subsequent quantification revealed that four metabolites, including Delphinidin-3-O-galactoside, Delphinidin-3-O-(6″-O-xylosyl)glucoside, Cyanidin-3-O-galactoside, and Pelargonidin-3-O-(xylosyl)glucoside, were the most highly accumulated in the ZY cultivar, suggesting their role in the purple pigmentation of ZY pea pods. There were 49 differentially accumulated anthocyanidins in ZY vs. FM, 43 differentially accumulated anthocyanidins in ZY vs. QZ, and 21 differentially accumulated anthocyanidins in FM vs. QZ. These findings highlight the importance of the type and concentration of anthocyanin compounds, especially those based on delphinidin, cyanidin, and pelargonidin, in the development of purple pea pods. The transcriptomic analysis revealed that certain anthocyanin biosynthetic genes were expressed at higher levels in ZY than in FM and QZ. In ZY, the higher expression levels of five key genes (PAL, 4CL, CHS, F3H, and UFGT) resulted in elevated anthocyanin content compared to FM and QZ. Furthermore, the BSA-seq analysis identified a candidate region associated with purple color in pea pods, which is located on chromosome 6 and contains 21 DEGs. Sequence variation in KIW84_061698, which encodes a bHLH transcription factor, was identified as the key candidate gene controlling anthocyanin content. This study clarifies the molecular mechanisms behind pea pod coloration and identifies potential genetic engineering targets for breeding anthocyanin-rich sugar snap peas. Full article
(This article belongs to the Special Issue Advances in Crop Molecular Breeding and Genetics—2nd Edition)
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25 pages, 11403 KB  
Article
Organic Acids Metabolic Response and Transcription Factor Expression Changes of Highland Barley Seedlings Under Na2SeO3 Treatment
by Xiaozhuo Wu, Huichun Xie, Jianxia Ma, Guigong Geng, Xiaoli Yang and Feng Qiao
Agriculture 2025, 15(13), 1364; https://doi.org/10.3390/agriculture15131364 - 25 Jun 2025
Viewed by 502
Abstract
Selenium (Se), as a vital trace element, plays an important role in regulating the antioxidant systems of plants, strengthening photosynthetic capacity, and enhancing their stress resistance. Selenate and selenite are the dominant forms of Se available to plants in soils. This research takes [...] Read more.
Selenium (Se), as a vital trace element, plays an important role in regulating the antioxidant systems of plants, strengthening photosynthetic capacity, and enhancing their stress resistance. Selenate and selenite are the dominant forms of Se available to plants in soils. This research takes highland barley as the research object, aiming to assess the impacts of plant growth, organic acid metabolite, and six transcription factor families in highland barley seedlings under varying concentrations of Na2SeO3. The study indicated that compared to the control group (CK), the plant height of highland barley seedlings under Se1 (0.02 g/kg Na2SeO3) treatment significantly increased by 66%. Under the Se2 (0.2 g/kg Na2SeO3) treatment, plant height significantly decreased by 28%. With Na2SeO3 concentration increased, the pigment content, O2 production rate, and soluble protein content in highland barley seedlings decreased, while the contents of soluble sugar, MDA, and H2O2 increased. Se1 treatment was found to be more beneficial for the growth and development of seedlings. The organic selenium in leaves and roots under Se2 treatment significantly increased by 1105-fold and 188-fold, respectively. The most effective migration capability from soil to leaf under Se1 or Se2 treatment was up to 6.15 or 6.56, respectively. Based on metabolomics, 30 differential metabolites of organic acids were screened from highland barley seedlings under Na2SeO3 treatment and showed positive correlationships with organic selenium, inorganic selenium, and total selenium in highland barley seedling leaves. Through transcriptome analysis, heatmap analysis on six major categories of transcription factors (bHLH, MYB, NAC, WRKY, GATA, and HSF) was performed. Under Se2 treatment, approximately two-thirds of the transcription factors showed high expressions. We further screened 26 differentially expressed genes (DEGs) related to Na2SeO3 concentration. Based on correlation analysis, there were six genes in the bHLH family, five in MYB, three in NAC, five in WRKY, and three in the GATA and HSF families that showed positive correlations with 30 differential organic acid metabolites. These results enhance our understanding of the relationship between the organic acid metabolites and transcription factor expression in highland barley seedlings under Na2SeO3 treatment. Full article
(This article belongs to the Section Crop Genetics, Genomics and Breeding)
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16 pages, 3566 KB  
Article
Effects of Dietary β-Carotene on the Gonadal Color, Pigmentation, and Regulation Mechanisms in Sea Urchin Strongylocentrotus Intermedius
by Weixiao Di, Yinuo Zhang, Huinan Zuo, Haijing Liu, Lina Wang, Jun Ding, Yaqing Chang and Rantao Zuo
Fishes 2025, 10(7), 304; https://doi.org/10.3390/fishes10070304 - 24 Jun 2025
Viewed by 729
Abstract
This study aims to clarify the dose–response relationship between dietary β-carotene levels and gonadal pigment deposition and regulation mechanisms related to the carotenoid synthesis of Strongylocentrotus intermedius based on a 60-day feeding trial and subsequent transcriptome analysis. Adult sea urchins (initial weight: 9.33 [...] Read more.
This study aims to clarify the dose–response relationship between dietary β-carotene levels and gonadal pigment deposition and regulation mechanisms related to the carotenoid synthesis of Strongylocentrotus intermedius based on a 60-day feeding trial and subsequent transcriptome analysis. Adult sea urchins (initial weight: 9.33 ± 0.21 g) of three cages were given one of the dry feeds with different doses of β-carotene (0 mg/kg, 150 mg/kg, 300 mg/kg) or fresh kelp (Saccharina japonica). The results indicated that the weight gain rate (WGR) of sea urchins increased with the addition of β-carotene, with that of the C300 group being markedly higher than that of the C0 group. The addition of β-carotene significantly improved the redness (a*) and yellowness (b*) values of the gonads, with sea urchins in the C300 group exhibiting closest gonad coloration to those in the kelp-fed group. Meanwhile, β-carotene and echinenone in the gonads of the C300 group showed the highest contents, reaching 1.96 μg/kg and 11.97 μg/kg, respectively. Several differential genes, enriched in the pathways of steroid biosynthesis, oxidative phosphorylation, and ubiquitination, were screened based on transcriptome analysis. Real-time PCR further demonstrated that β-carotene significantly upregulated the expression of cholesterol 25-hydroxylase (CH25H), NADH dehydrogenase subunit 1 (ND1), NADH dehydrogenase subunit 2 (ND2), and NADH dehydrogenase subunit 4 (ND4) while it downregulated the expression of 24-dehydrocholesterol reductase (DHCR24). These results showed that 300 mg/kg β-carotene significantly increased the WGR, redness, and yellowness values, as well as the contents of β-carotene and echinenone in the gonads of S. intermedius. On the one hand, dietary β-carotene increased NADH enzyme activity, which participates in echinenone synthesis by donating electrons for the transformation of β-carotene to echinenone synthesis. On the other hand, the addition of β-carotene inhibited cholesterol synthesis by increasing the expression of CH25H and decreasing the expression of DHCR24, which could in turn increase the fluidity and permeability of the cell membranes and the transport efficiency of β-carotene and echinenone from the digestive tract to the gonads. These results provided fundamental insights into the production of sea urchin gonads with market-favored colors. Full article
(This article belongs to the Special Issue Advances in Aquaculture Feed Additives)
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20 pages, 6424 KB  
Article
Combined Multi-Omics and Co-Expression Network Analyses Uncover the Pigment Accumulation Mechanism of Orange-Red Petals in Brassica napus L.
by Ledong Jia, Shengting Li, Chao Zhang, Lijun Zeng, Shulin Shen, Nengwen Yin, Huiyan Zhao, Zhanglin Tang, Cunmin Qu, Jiana Li and Zhiyou Chen
Biology 2025, 14(6), 693; https://doi.org/10.3390/biology14060693 - 13 Jun 2025
Cited by 1 | Viewed by 753
Abstract
Rapeseed (Brassica napus L.) has been cultivated as an ornamental plant in recent years. However, the metabolic and regulatory processes involved in pigment accumulation in. B. napus flowers are poorly understood. To address this knowledge gap, we conducted a multi-omics analysis of [...] Read more.
Rapeseed (Brassica napus L.) has been cultivated as an ornamental plant in recent years. However, the metabolic and regulatory processes involved in pigment accumulation in. B. napus flowers are poorly understood. To address this knowledge gap, we conducted a multi-omics analysis of the orange-red-flowered ‘OrP’ and the yellow-flowered ‘ZS11’ rapeseed cultivars. The total anthocyanin content of ‘OrP’ petals was 5.420-fold and 3.345-fold higher than ‘ZS11’ petals at the S2 and S4 developmental stages, respectively. The red coloration of ‘OrP’ flowers resulted primarily from the presence of anthocyanin pigment derivatives. The up-regulated differentially expressed genes (DEGs) of four stages in ‘OrP’ were found to be significantly enriched in phenylpropanoid, flavonoid, and anthocyanin metabolism-associated GO and KEGG terms. Weighted Gene Co-expression Network Analysis (WGCNA) revealed that 51 DEGs were linked to anthocyanin metabolism, including several structural genes such as BnaCHS, BnaF3H, BnaF3′H, BnaCHS, BnaDFR, BnaANS, BnaUGTs, and the transcription factor (TF) genes BnaHY5, BnaBBX22, BnaPIL1, BnaPAP2, BnaTT8, BnaTTG2, and BnaMYBL2. Furthermore, we found that three main factors affecting the relative content of anthocyanins in petals were likely responsible for the fading of ‘OrP’ petals, namely the significantly down-regulated expression of genes (BnaDFR, BnaANS, BnaPAP2, BnaTT8, and BnaTTG2) related to anthocyanin biosynthesis, the significantly up-regulated expression of genes (Bna.BGLUs, Bna.PRXs, and BnaMYBL2) related to anthocyanin degradation or the negative regulation of anthocyanin biosynthesis, and the rapidly increasing petals area. Full article
(This article belongs to the Special Issue The Potential of Genetics and Plant Breeding in Crop Improvement)
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Article
Cesium Accumulation Patterns and Stress Response in Hydroponic Radish (Raphanus sativus L.): A Physiological–Transcriptomic Study
by Yu-Han Wen, Xi Chen, Ming Sun, Chao-Hui Yang, Meng-Yuan Xu, Feng-Xiang Lai, Si-Qi Fu, Yu-Meng Fan, Xin-Peng Guo, Qun Li and Guo Wu
Plants 2025, 14(12), 1802; https://doi.org/10.3390/plants14121802 - 12 Jun 2025
Cited by 1 | Viewed by 1385
Abstract
The present study systematically investigated the cesium (Cs) enrichment characteristics and physiological responses to Cs exposure in radish (Raphanus sativus L.) seedlings under hydroponic conditions through integrated physiological, biochemical, and transcriptome analyses. The results showed that the Cs content in radish roots, [...] Read more.
The present study systematically investigated the cesium (Cs) enrichment characteristics and physiological responses to Cs exposure in radish (Raphanus sativus L.) seedlings under hydroponic conditions through integrated physiological, biochemical, and transcriptome analyses. The results showed that the Cs content in radish roots, stems, and cotyledons increased progressively with rising Cs concentrations (0.25–2 mM), and Cs mainly accumulated in the cotyledon. The transfer factor (TF) increased by 63.29% (TF = 3.87) as the Cs concentration increased from 0.25 to 2 mM, while the biological concentration factor (BCF) decreased by 72.56% (BCF = 14.87). Severe growth inhibition was observed at 2 mM Cs stress, with biomass reduction reaching 29.73%. The carotenoid content decreased by 11.92%; however, the total chlorophyll content did not change significantly, and the photosynthesis of radish was not affected. In addition, Cs exposure disrupted mineral nutrient homeostasis, decreasing potassium (K), sodium (Na), magnesium (Mg), and iron (Fe) content. The superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities, reactive oxygen species (ROS), and malondialdehyde (MDA) content increased under the different Cs treatments, which indicated that Cs exposure induced oxidative stress response in radish seedlings. Transcriptome analysis detected a total of 4326 differentially expressed genes (DEGs), in which altered expression patterns in genes associated with mineral transport, antioxidant systems, and carotenoid biosynthesis pathways in radish under 2 mM Cs treatment were observed. In conclusion, this study comprehensively investigated the physiological and molecular responses of radish to Cs stress, revealing that Cs accumulation exhibited site-specific preference and concentration dependence and induced physiological disturbances, including growth inhibition and photosynthetic pigment metabolism alterations. At the transcription level, Cs activated the enzymatic antioxidant system, related genes, and stress-response pathways. Notably, this study is the first to demonstrate that Cs disrupts plant mineral nutrition homeostasis and inhibits carotenoid biosynthesis. These findings establish a crucial theoretical foundation for utilizing radish in Cs-contaminated phytoremediation strategies. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Responses to Heavy Metal Stress)
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