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Keywords = IMF deposition

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17 pages, 9983 KiB  
Article
Integrated Multi-Omics of the Longissimus Dorsal Muscle Transcriptomics and Metabolomics Reveals Intramuscular Fat Accumulation Mechanism with Diet Energy Differences in Yaks
by Jingying Deng, Pengjia Bao, Ning Li, Siyuan Kong, Tong Wang, Minghao Zhang, Qinran Yu, Xinyu Cao, Jianlei Jia and Ping Yan
Biomolecules 2025, 15(7), 1025; https://doi.org/10.3390/biom15071025 - 16 Jul 2025
Viewed by 243
Abstract
IMF (intramuscular fat, IMF), as a key index for evaluating meat quality traits (shear force and cooking loss, etc.), and its deposition process are jointly regulated by nutritional and genetic factors. In this study, we analyzed the molecular regulation mechanism of IMF deposition [...] Read more.
IMF (intramuscular fat, IMF), as a key index for evaluating meat quality traits (shear force and cooking loss, etc.), and its deposition process are jointly regulated by nutritional and genetic factors. In this study, we analyzed the molecular regulation mechanism of IMF deposition in the LD (longissimus dorsal muscle, LD) by dietary energy level in Pamir yaks. Meat quality assessment showed that the meat quality of the High-energy diet group (1.53 MJ/Kg, G) and the Medium-energy diet group (1.38 MJ/Kg, Z) were significantly improved compared with that of the Low-energy diet group (0.75 MJ/Kg, C), in which IMF content in the LD of yaks in G group was significantly higher (p < 0.05) compared with Z and C groups. Further analysis by combined transcriptomics and lipid metabolomics revealed that the differences in IMF deposition mainly originated from the metabolism of lipids, such as TG (triglycerides, TG), PS (phosphatidylserine, PS), and LPC (lysophosphatidylcholine, LPC), and were influenced by SFRP4, FABP4, GADD45A, PDGFRA, RBP4, and DGAT2 genes, further confirming the importance of lipid–gene interactions in IMF deposition. This study reveals the energy-dependent epigenetic regulatory mechanism of IMF deposition in plateau ruminants, which provides molecular targets for optimizing yak nutritional strategies and quality meat production, while having important theoretical and practical value for the sustainable development of livestock husbandry on the Tibetan Plateau. Full article
(This article belongs to the Section Molecular Genetics)
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20 pages, 10457 KiB  
Article
Unveiling the Regulatory Mechanism of Tibetan Pigs Adipogenesis Mediated by WNT16: From Differential Phenotypes to the Application of Multi-Omics Approaches
by Qiuyan Huang, Kunli Zhang, Fanming Meng, Sen Lin, Chun Hong, Xinming Li, Baohong Li, Jie Wu, Haiyun Xin, Chuanhuo Hu, Xiangxing Zhu, Dongsheng Tang, Yangli Pei and Sutian Wang
Animals 2025, 15(13), 1904; https://doi.org/10.3390/ani15131904 - 27 Jun 2025
Viewed by 379
Abstract
The aim of this study is to investigate the physiological characteristics and regulatory mechanisms of porcine intramuscular fat (IMF), subcutaneous fat (take back fat (BF), for example), and visceral fat (take perienteric fat (PF), for example) to address the challenge of optimizing meat [...] Read more.
The aim of this study is to investigate the physiological characteristics and regulatory mechanisms of porcine intramuscular fat (IMF), subcutaneous fat (take back fat (BF), for example), and visceral fat (take perienteric fat (PF), for example) to address the challenge of optimizing meat quality without excessive fat deposition. Many improved breed pigs have fast growth rates, high lean meat rates, and low subcutaneous fat deposits, but they also have low IMF content, resulting in poor meat quality. There is usually a positive correlation between intramuscular fat and subcutaneous fat deposits. This study selected eight-month-old female Tibetan pigs as experimental subjects. After slaughter, fat samples were collected. Histological differences in adipocyte morphology were observed via hematoxylin–eosin (HE) staining of tissue sections, and phenotypic characteristics of different adipose tissues were analyzed through fatty acid composition determination. Transcriptome sequencing and untargeted metabolomics were employed to perform pairwise comparisons between different fatty tissues to identify differentially expressed genes and metabolites. A siRNA interference model was constructed and combined with Oil Red O staining and lipid droplet optical density measurement to investigate the regulatory role of WNT16 in adipocyte differentiation. Comparative analysis of phenotypic and fatty acid composition differences in adipocytes from different locations revealed that IMF adipocytes have significantly smaller areas and diameters compared to other fat depots and contain higher levels of monounsaturated fatty acids. Integrated transcriptomic and metabolomic analyses identified differential expression of WNT16 and L-tyrosine, both of which are involved in the melanogenesis pathway. Functional validation showed that inhibiting WNT16 in porcine preadipocytes downregulated adipogenic regulators and reduced lipid droplet accumulation. This cross-level regulatory mechanism of “phenotype detection–multi-omics analysis–gene function research” highlighted WNT16 as a potential key regulator of site-specific fat deposition, providing new molecular targets for optimizing meat quality through nutritional regulation and genetic modification. Full article
(This article belongs to the Section Pigs)
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14 pages, 2823 KiB  
Article
LincRNA-MSTRG.673.2 Promotes Chicken Intramuscular Adipocyte Differentiation by Sponging miR-128-3p
by Binbin Zhang, Shuaipeng Zhu, Yuehua He, Wenjie Liang, Tingqi Zhu, Ruili Han, Donghua Li, Yanbin Wang, Yadong Tian, Guoxi Li, Xiangtao Kang, Wenting Li and Guirong Sun
Animals 2025, 15(13), 1879; https://doi.org/10.3390/ani15131879 - 25 Jun 2025
Viewed by 379
Abstract
Background: Intramuscular fat content is positively correlated with meat flavor and juiciness. Increasing the intramuscular fat (IMF) content of chickens while increasing their growth rate has become a hot topic in molecular breeding. The group’s previous studies showed that miR-128-3p inhibited chicken intramuscular [...] Read more.
Background: Intramuscular fat content is positively correlated with meat flavor and juiciness. Increasing the intramuscular fat (IMF) content of chickens while increasing their growth rate has become a hot topic in molecular breeding. The group’s previous studies showed that miR-128-3p inhibited chicken intramuscular adipocyte differentiation and lipogenesis. However, the regulatory mechanism of miR-128-3p in intramuscular preadipocytes is currently unknown. In this study, we investigated the mechanism of miR-128-3p regulation of chicken intramuscular adipocyte differentiation and deposition. Results: Transcriptome data analysis of differential LincRNAs indicated that, compared to the NC group, the mimics-treated group had seventeen significantly differentially expressed LincRNAs (p < 0.05), including six upregulated and eleven downregulated ones; the inhibitor-treated group had seventeen differentially expressed LincRNAs (p < 0.05), including eight upregulated and nine downregulated ones; and twenty-four differentially expressed LincRNAs (p < 0.05) were observed when comparing the mimics-treated group to the inhibitor-treated group, with fourteen upregulated and ten downregulated ones. Functional enrichment analysis revealed that DELincRNAs from the overexpression group (M group) and interference group (SI group) were involved in the negative regulation of metabolic processes, response to steroid hormones, and regulation of actin cytoskeleton. Furthermore, target gene prediction analysis showed that miR-128-3p can target many of the DELincRNAs, such as LincRNA-MSTRG.673.2, LincRNA-MSTRG.39.2, LincRNA-MSTRG.39.3, and LincRNA-MSTRG.14270.2. LincRNA-MSTRG.673.2 was predominantly expressed in the cytoplasm of intramuscular adipocytes. Dual luciferase reporter identified the targeting relationship between miR-128-3p and LincRNA-MSTRG.673.2. The results of subsequent functional assays demonstrated that interfering with MSTRG.673.2 has been shown to inhibit lipid deposition in intramuscular preadipocytes. Transfection experiments have shown that LincRNA-MSTRG.673.2 can affect the expression of miR-128-3p. Conclusions: This study found that LincRNA-MSTRG.673.2 promoted chicken intramuscular adipocyte differentiation by downregulating miR-128-3p. The results are noteworthy for improving chicken meat quality, molecular breeding, and lipid metabolism research. Full article
(This article belongs to the Section Poultry)
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13 pages, 4529 KiB  
Article
Variation in Intramuscular Fat Deposition of Goats and Sheep and Its Correlation with Gut Microbiota
by Lei Yang, Shaobin Li, Jiagong Hou, Zhisheng Tang, Bingang Shi, Yuzhu Luo, Jiqing Wang and Fangfang Zhao
Foods 2025, 14(11), 1885; https://doi.org/10.3390/foods14111885 - 26 May 2025
Viewed by 581
Abstract
The meat quality of sheep and goats differs even within the same age, gender, and farming systems. Intramuscular fat (IMF) content is an important factor affecting the quality of livestock meat because it affects muscle color, tenderness, juiciness, water-holding capacity, and flavor. This [...] Read more.
The meat quality of sheep and goats differs even within the same age, gender, and farming systems. Intramuscular fat (IMF) content is an important factor affecting the quality of livestock meat because it affects muscle color, tenderness, juiciness, water-holding capacity, and flavor. This study evaluates the differences in IMF deposition characteristics between Longdong cashmere goats and Tan sheep, and also explores the correlations between these variations and the gut microbiota. The results revealed that the IMF contents in shoulder and rump meat, as well as the blood lipid levels, of Longdong cashmere goats were higher than those of Tan sheep (p < 0.05). The content of fatty acid synthase (FAS) in the duodenum of the goats was lower, but the content of hormone-sensitive lipase (HSL) in both the pancreas and duodenum was greater (p < 0.05). The Chao1 and β diversity showed differences between the two breeds, observed not only in the abomasum but also in the colon. The specific microbiota identified from the goats were involved in the lipid metabolism pathway. The concentrations of acetic acid and propionic acid in the colonic and abomasal chyme were decreased in the goats when compared to the sheep (p < 0.05). The contents of FAS in the colonic chyme of the goats were significantly lower, while HSL in the abomasal chyme was significantly higher than that of the sheep. The correlation analysis of IMF deposition with gut microbiota showed that Acetobacter and UBA1711 in the abomasum, as well as Faecousia, WQUU01, UBA5905, and GCA-900066495 in the colon, were positively correlated with the IMF content in shoulder meat and the level of LDL (except for UBA1711), but negatively associated with the content of propionic acid (|r| > 0.45, p < 0.05). This preliminary study has demonstrated that some specific bacteria in the abomasum and colon were associated with IMF deposition, while also providing an indicative reference range for further investigation into the effects of microbes on IMF deposition. Full article
(This article belongs to the Section Meat)
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18 pages, 5475 KiB  
Article
Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle
by Siwei Wang, Tingting Liu, Peng Peng, Yurong Fu, Shaoqing Shi, Shuang Liang, Xi Chen, Kun Wang and Rongyan Zhou
Animals 2025, 15(9), 1306; https://doi.org/10.3390/ani15091306 - 30 Apr 2025
Cited by 1 | Viewed by 541
Abstract
Intramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the [...] Read more.
Intramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the molecular mechanisms governing IMF regulation in these crossbreeds remain poorly understood. To elucidate the mechanism of IMF deposition in these crossbred cattle, we conducted a comparative transcriptomic analysis of longissimus dorsi muscles and livers from cattle with divergent IMF content. RNA-seq revealed 940 and 429 differentially expressed genes (DEGs) in the liver and muscle, respectively, with 60 genes co-differentially expressed (co-DEGs) in both tissues. Functional enrichment highlighted lipid metabolism pathways including fatty acid β-oxidation, PPAR signaling, and glycerolipid metabolism. A total of eleven genes including ACAA2, ACADL, ACOX2, CPT1B, CPT2, LPL, SLC27A1, ACAT1, GK, ACOX3, and ACSM5, were screened as key candidate genes for IMF deposition. A “liver–muscle” regulatory network of IMF deposition was built to illustrate the tissues’ interaction. The reliability of the transcriptomic data was verified by quantitative reverse real-time PCR (qRT-PCR). Our findings provide novel molecular markers for increasing the IMF content and accelerating the genetic improvement of beef quality traits in crossbred cattle. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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21 pages, 4590 KiB  
Article
Identification of Key Genes Related to Intramuscular Fat Content of Psoas Major Muscle in Saba Pigs by Integrating Bioinformatics and Machine Learning Based on Transcriptome Data
by Zixia Huang, Yongli Yang, Jinhua Lai, Qiang Chen, Xiaoyi Wang, Shuyan Wang, Mingli Li and Shaoxiong Lu
Animals 2025, 15(8), 1181; https://doi.org/10.3390/ani15081181 - 20 Apr 2025
Viewed by 595
Abstract
The psoas major muscle (PMM) is a piece of pork with good tenderness and high value. Intramuscular fat (IMF) content, serving as a pivotal indicator of pork quality, varies greatly among pigs within the same breed. However, there is a paucity of studies [...] Read more.
The psoas major muscle (PMM) is a piece of pork with good tenderness and high value. Intramuscular fat (IMF) content, serving as a pivotal indicator of pork quality, varies greatly among pigs within the same breed. However, there is a paucity of studies focusing on investigating the molecular mechanism of PMM IMF deposition in the same pig breed. The present study aimed to identify the potential genes related to the IMF content of PMM in low- and high-IMF Saba pigs based on transcriptome data analysis. The data used in this study were the RNA sequences of PMM from 12 Saba pigs (PRJNA1223630, from our laboratory) and gene expression profiles (GSE207279) acquired from the NCBI Sequence Read Archive database and the GEO database, respectively, together with data on the fatty acid and amino acid composition of the 12 Saba pigs’ PMM. It was found that the high-IMF pigs exhibited significantly elevated levels of saturated fatty acids and (mono)unsaturated fatty acids, especially C14:0, C16:0, C20:0, C16:1, C18:1n9c, and C20:2, compared with those in the low-IMF pigs (p < 0.05 or p < 0.01). A total of 370 differentially expressed genes (DEGs) (221 up- and 149 down-regulated) were identified based on PRJNA1223630. Then, 20 hub genes were identified through protein–protein interaction (PPI) network analysis. Four potential fat-deposition-related genes (DGAT2, PCK1, MELK, and FASN) were further screened via the intersection of the candidate genes identified by the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm and the top five genes ranked by the Random Forest (RF) method based on the 20 hub genes and were validated in the test gene set (GSE207279). The constructed mRNA (gene)–miRNA–lncRNA network, involving miRNAs (miR-103a-3p, miR-107, and miR-485-5p), lncRNAs (XIST, NEAT1, and KCNQ1OT1), and FASN, might be crucial for IMF deposition in pigs. These findings might delineate valuable regulatory molecular mechanisms coordinating IMF deposition and could serve as a beneficial foundation for the genetic improvement of pork quality. Full article
(This article belongs to the Section Pigs)
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15 pages, 2676 KiB  
Article
Ssc-miR-130b Enhances Cell Proliferation and Represses Adipogenesis of Primary Cultured Intramuscular Preadipocytes in Pigs
by Yunqiu Yang, Yongfang Chen, Lijun Wang, Min Du, Rui Zhang, Yao Lu and Shifeng Pan
Vet. Sci. 2025, 12(4), 375; https://doi.org/10.3390/vetsci12040375 - 17 Apr 2025
Viewed by 541
Abstract
In the efforts towards germplasm innovation of livestock and poultry, strategies to improve meat quality have faced some increasingly challenging and dynamic concerns. Intramuscular fat (IMF) content and backfat thickness are two important traits contributing to meat quality. MicroRNAs (miRNAs)—a class of endogenous [...] Read more.
In the efforts towards germplasm innovation of livestock and poultry, strategies to improve meat quality have faced some increasingly challenging and dynamic concerns. Intramuscular fat (IMF) content and backfat thickness are two important traits contributing to meat quality. MicroRNAs (miRNAs)—a class of endogenous noncoding RNAs maintaining cell homeostasis by inhibiting target gene expression—have been proven as critical regulators of body fat deposition, thus affecting farm animal production. Our previous in vitro and in vivo models of pigs have clarified that miR-130b overexpression can obviously suppress adipogenesis of subcutaneous preadipocytes and lower backfat thickness. However, the way miR-130b regulates proliferation and adipogenesis of primary cultured porcine intramuscular preadipocytes (PIMPA) and the underlying mechanism are still unknown. PIMPA derived from longissimus dorsi muscle were employed to examine the role of miR-130b in proliferation and adipogenesis and to further elucidate its underlying mechanism. Lipid deposition in cytoplasm was evaluated by TG quantification and ORO-staining, and EDU-staining was employed to measure cell proliferation. Adipogenic and proliferation-related gene expression were conducted by qPCR and Western blot. MiR-130b overexpression markedly stimulated proliferation of PIMPA by increasing cell cycle-related gene expression. Furthermore, overexpression of miR-130b significantly inhibited adipogenic differentiation of PIMPA, mainly by inhibiting expression of adipogenic differentiation marker genes PPAR-γ and SREBP1. In addition, we proved that miR-130b significantly inhibited expression of PPAR-γ downstream target genes and ultimately repressed adipogenesis. Ssc-miR-130b accelerated proliferation but inhibited adipogenic differentiation of PIMPA, contributing to an enhanced knowledge of the function of ssc-miR-130b in lipid deposition, and providing potential implications for enhancing pork quality. Full article
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19 pages, 2901 KiB  
Article
SIRT5 Regulates Lipid Deposition in Goat Preadipocytes via PI3K-Akt and MAPK Signaling Pathways
by Haiyang Li, Wenli Yao, Changheng Yang, Wenyang Zhang, Yong Wang, Yaqiu Lin, Zhanyu Du, Changhui Zhang, Lian Huang, Ming Zhang, Huaigong Fan, Jiangjiang Zhu and Hua Xiang
Animals 2025, 15(7), 1072; https://doi.org/10.3390/ani15071072 - 7 Apr 2025
Viewed by 609
Abstract
Silent Information Regulator 5 (SIRT5) has been established as a crucial regulator of cellular alanylation modification. Furthermore, accumulating evidence suggests that SIRT5 plays a significant regulatory role in key metabolic pathways, including glycolysis, the tricarboxylic acid (TCA) cycle, and fatty acid [...] Read more.
Silent Information Regulator 5 (SIRT5) has been established as a crucial regulator of cellular alanylation modification. Furthermore, accumulating evidence suggests that SIRT5 plays a significant regulatory role in key metabolic pathways, including glycolysis, the tricarboxylic acid (TCA) cycle, and fatty acid oxidation, all of which are closely associated with cellular lipid metabolism. Despite these advancements, the specific role of SIRT5 in regulating intramuscular fat (IMF) deposition in goats, as well as the underlying molecular mechanisms, remains largely unexplored. In this study, we cloned the complete coding sequence of the goat SIRT5 gene and, through amino acid sequence alignment, demonstrated its closest phylogenetic relationship with sheep. Additionally, we characterized the higher expression of SIRT5 during the differentiation of goat intramuscular precursor adipocytes. The silencing of SIRT5 by siRNA-mediated knockdown significantly upregulated the expression of lipogenesis-related genes and enhanced lipid deposition in goat intramuscular preadipocytes. Concurrently, SIRT5 deficiency led to the inhibition of cell proliferation and a marked reduction in apoptosis. Interestingly, although overexpression of SIRT5 promoted cell proliferation, it did not significantly alter lipid deposition in goat intramuscular precursor adipocytes. RNA sequencing (RNA-seq) analysis identified a total of 106 differentially expressed genes (DEGs) following SIRT5 silencing in goat preadipocytes, predominantly involved in the Focal adhesion, HIF-1, PI3K-Akt, and MAPK signaling pathways by KEGG pathway enrichment analysis. Notably, we successfully reversed the phenotypic effects observed in SIRT5 knockdown goat precursor adipocytes by inhibiting the PI3K-Akt and MAPK signaling pathways using the AKT inhibitor LY294002 and the p38 MAPK pathway inhibitor PD169316, respectively. In conclusion, our findings demonstrated that SIRT5 may modulate intramuscular fat deposition in goats through PI3k-Akt and MAPK signaling pathways. These results expand the gene regulatory network associated with IMF formation and provide a theoretical foundation for improving meat quality by targeting IMF deposition. Full article
(This article belongs to the Special Issue Livestock and Poultry Genetics and Breeding Management)
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25 pages, 31779 KiB  
Article
Transcriptomic Analysis of Muscle Satellite Cell Regulation on Intramuscular Preadipocyte Differentiation in Tan Sheep
by Xiaochun Xu, Cong Zhan, Jiaqi Qiao, Yuxuan Yang, Changyuan Li, Pan Li and Sen Ma
Int. J. Mol. Sci. 2025, 26(7), 3414; https://doi.org/10.3390/ijms26073414 - 5 Apr 2025
Cited by 1 | Viewed by 617
Abstract
Intramuscular fat (IMF) content is a key factor influencing meat properties including tenderness, flavor, and marbling. However, the complex molecular mechanisms regulating IMF deposition, especially the interactions between intramuscular preadipocytes (IMAdCs) and skeletal muscle satellite cells (SMSCs), remain unclear. In this study, a [...] Read more.
Intramuscular fat (IMF) content is a key factor influencing meat properties including tenderness, flavor, and marbling. However, the complex molecular mechanisms regulating IMF deposition, especially the interactions between intramuscular preadipocytes (IMAdCs) and skeletal muscle satellite cells (SMSCs), remain unclear. In this study, a direct co-culture system of sheep IMAdCs and SMSCs was used to elucidate their intercellular interactions. RNA sequencing and bioinformatics analyses were performed under monoculture and co-culture conditions for later stages of differentiation. The obtained results showed that SMSCs significantly inhibited the adipogenic capacity of IMAdCs. This was reflected in the co-culture markedly altered gene expression and observations of lipid droplets in our studies, i.e., the PPARG, ACOX2, PIK3R1, FABP5, FYN, ALDOC, PFKM, PFKL, HADH, and HADHB genes were down-regulated in the co-cultured IMAdCs in association with the inhibition of fat deposition, whereas ACSL3, ACSL4, ATF3, EGR1, and IGF1R within the genes upregulated in co-culture IMAdCs were associated with the promotion of lipid metabolism. In addition, GO, KEGG, and ligand–receptor pairing analyses further elucidated the molecular mechanisms of intercellular communication. These findings emphasize the regulatory role of SMSCs on intramuscular preadipocyte differentiation and lipid metabolism, providing a theoretical framework for targeted molecular strategies to improve sheep meat quality. Full article
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15 pages, 1624 KiB  
Communication
Genetic Diversity Estimation and Genome-Wide Selective Sweep Analysis of the Bazhou Yak
by Baigao Yang, Hang Zhang, Xiaoyi Feng, Zhou Yu, Jianhua Cao, Yifan Niu, Pengcheng Wan, Gang Liu and Xueming Zhao
Animals 2025, 15(6), 849; https://doi.org/10.3390/ani15060849 - 15 Mar 2025
Viewed by 818
Abstract
The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding its phylogenetic history and genomic composition has hindered its long-term conservation [...] Read more.
The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding its phylogenetic history and genomic composition has hindered its long-term conservation and utilization. This study evaluated the genetic diversity, population phylogenetics, and genome-wide selective sweep analysis (GWSA) of 100 newly obtained Bazhou yaks through genome resequencing, as well as 340 public yak genomes from nine other populations on the Qinghai–Tibet Plateau. The results revealed moderate diversity, lower genomic inbreeding levels, and rapid linkage disequilibrium (LD) decay in Bazhou yaks. Principal component analysis (PCA) and phylogenetic analysis showed a clear separation of Bazhou yaks from other yak populations, indicating the Bazhou yak as an independent genetic population. Furthermore, less genetic differentiation was found between the Bazhou yak and the Huanhu yak, while ADMIXTURE analysis revealed a common ancestral lineage between Bazhou yaks and Huanhu yaks, indicating an important genetic contribution of the Qinghai yak population to Bazhou yaks. The GWSA identified a total of 833 selected genes in Bazhou yaks using the top 5% interaction windows of both parameters (FST, Pi ratio, and XP-EHH). A significant number of these genes are related to fat synthesis and deposition, such as MTOR, APOA1, and GPAT4. In summary, this study sheds light on the phylogenetic status and distinctive genomic features of Bazhou yaks, which facilitates our understanding of the genetic basis of the IMF phenotype in Bazhou yaks. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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17 pages, 7189 KiB  
Article
Circ_0011446 Regulates Intramuscular Adipocyte Differentiation in Goats via the miR-27a-5p/FAM49B Axis
by Jian-Mei Wang, Jin-Shi Lv, Ke-Han Liu, Yan-Yan Li, Jiang-Jiang Zhu, Yan Xiong, Yong Wang and Ya-Qiu Lin
Int. J. Mol. Sci. 2025, 26(5), 2294; https://doi.org/10.3390/ijms26052294 - 5 Mar 2025
Viewed by 897
Abstract
Intramuscular fat (IMF), or marbling, is a critical indicator of goat meat quality. Non-coding RNAs play a key role in the formation and deposition of IMF in vertebrates by regulating genes involved in its synthesis, degradation, and transport. The competing endogenous RNA (ceRNA) [...] Read more.
Intramuscular fat (IMF), or marbling, is a critical indicator of goat meat quality. Non-coding RNAs play a key role in the formation and deposition of IMF in vertebrates by regulating genes involved in its synthesis, degradation, and transport. The competing endogenous RNA (ceRNA) hypothesis identifies circular RNAs (circRNAs) as natural “sponges” for microRNAs (miRNAs). However, the precise mechanisms of circRNAs in goat IMF remain poorly understood. In the current study, we utilized existing sequencing data to construct a ceRNA regulatory network associated with intramuscular adipogenesis and fat deposition in goats. Our goal was to elucidate the post-transcriptional regulatory mechanism of family with sequence similarity 49 member B (FAM49B). Functionally, FAM49B was found to inhibit the differentiation of intramuscular preadipocytes and to directly interact with miR-27a-5p. Mechanistically, dual-luciferase reporter assays and quantitative real-time PCR (qRT-PCR) confirmed the interaction between circ0011446 and miR-27a-5p. Circ0011446 enhanced the expression of FAM49B mRNA and protein through post-transcriptional regulation. As a ceRNA, circ0011446 competitively binds miR-27a-5p, preventing miR-27a-5p from degrading FAM49B. In conclusion, our findings demonstrate that circ0011446 suppresses goat adipogenic differentiation of intramuscular preadipocytes by regulating the expression of the downstream target gene FAM49B through miR-27a-5p sequestration. This study provides a reference for goat meat quality or livestock breeding. Full article
(This article belongs to the Section Molecular Biology)
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15 pages, 470 KiB  
Article
Evaluation of Effect of Dietary Supplementation with Microencapsulated Hydrolyzed Tannins on Growth, Slaughter Performance, Meat Quality, and Lipid Metabolism of Zhongshan Shelducks
by Zhimei Tian, Zhengwei Tian, Yingshan Yin, Yongmei Wu, Zhenyuan Li, Qiaohua Liang, Miao Yu, Yiyan Cui, Xianyong Ma, Guanghui Peng and Zhenming Li
Foods 2025, 14(5), 839; https://doi.org/10.3390/foods14050839 - 28 Feb 2025
Viewed by 847
Abstract
This study investigated the effects of microenapsulated hydrolyzed tannins (MHTs) on the growth performance and meat quality of Zhongshan shelducks. A total of 288 healthy Zhongshan shelducks with an average initial weight of 1790.27 ± 0.14 kg were randomly divided into four groups [...] Read more.
This study investigated the effects of microenapsulated hydrolyzed tannins (MHTs) on the growth performance and meat quality of Zhongshan shelducks. A total of 288 healthy Zhongshan shelducks with an average initial weight of 1790.27 ± 0.14 kg were randomly divided into four groups through a 56 d experiment period and were fed a basal diet supplemented with 0 (CON), 400, 800, and 1600 mg/kg MHTs, respectively. Results showed that 400 and 800 mg/kg MHTs improved the final body weight, average daily gain, glutathione peroxidase activity, and total antioxidant capacity compared to CON (p ≤ 0.05). The diet supplemented with 400 mg/kg MHTs decreased shear force and 800 mg/kg MHTs increased the yield of pectoralis major muscle compared to CON (p ≤ 0.05). Dietary MHTs increased inosine monophosphate content and decreased percentage C14:0 content in meat; however, the b*45 min value, 48 h drip loss, and shear force were increased but the percentage intramuscular fat (IMF) content was decreased in pectoralis major muscle with the increase in MHTs (p ≤ 0.05). Compared to CON, 400 and 800 mg/kg MHTs increased the percentage content of IMF, C18:1n-9, C18:2n-6, monounsaturated fatty acids, polyunsaturated fatty acids, and unsaturated fatty acids in pectoralis major muscle (p ≤ 0.05). Furthermore, 400 and 800 mg/kg MHTs improved the lipid metabolism of IMF deposition, fatty acid uptake, and adipogenesis by activating the peroxisome proliferator-activated receptor gamma pathway to regulate fatty acid synthetase and lipoprotein lipase genes. In conclusion, diets supplemented with 400 and 800 mg/kg MHTs could improve growth, meat quality, antioxidant capacity, and lipid metabolism in Zhongshan shelducks. Full article
(This article belongs to the Section Meat)
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13 pages, 2579 KiB  
Article
Analysis of Transcriptome Differences Between Subcutaneous and Intramuscular Adipose Tissue of Tibetan Pigs
by Xinming Li, Qiuyan Huang, Fanming Meng, Chun Hong, Baohong Li, Yecheng Yang, Zixiao Qu, Junda Wu, Fei Li, Haiyun Xin, Bin Hu, Jie Wu, Chuanhuo Hu, Xiangxing Zhu, Dongsheng Tang, Zongliang Du and Sutian Wang
Genes 2025, 16(3), 246; https://doi.org/10.3390/genes16030246 - 20 Feb 2025
Cited by 1 | Viewed by 955
Abstract
Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique [...] Read more.
Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique fat metabolism pattern due to long-term adaptation to harsh environments. This makes it an excellent genetic and physiological model for investigating fat deposition characteristics. Adipose tissue from different body regions displays varying morphologies, cytokines, and adipokines. This study aimed to examine adipose tissue deposition characteristics in different parts of Tibetan pigs and provide additional data to explore the underlying mechanisms of differential fat deposition. Methods: Our research identified significant differences in the morphology and gene expression patterns between subcutaneous fat (abdominal fat [AF] and back fat [BF]) and intramuscular fat (IMF) in Tibetan pigs. Results: Histological observations revealed that subcutaneous fat cells were significantly larger in area and diameter compared to IMF cells. The transcriptomic analysis further identified differentially expressed genes (DEGs) between subcutaneous fat and IMF, with a total of 65 DEGs in BF vs. IMF and 347 DEGs in AF vs. IMF, including 25 DEGs common to both comparisons. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these genes were significantly associated with lipid metabolism-related signaling pathways, such as the Wnt, mTOR, and PI3K-Akt signaling pathways. Several DEGs, including DDAH1, ADRA1B, SLCO3A1, and THBS3, may be linked to the differences in fat deposition in different parts of Tibetan pigs, thereby affecting meat quality and nutritional value. Conclusions: These findings provide new insights into the unique fat distribution and deposition characteristics of Tibetan pigs and establish a foundation for breeding strategies aimed at improving pork quality. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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17 pages, 3728 KiB  
Article
Lipidomics and Transcriptomics Revealed Dietary Complex Plant Extracts Improve Lipid Composition of Longissimus dorsi Muscle in Sheep
by Hui Guo, Ruixue Nie, Wenwen Wang, Tao Guo, Chang Gao, Jinju Mao, Yuchao Hu, Na Liu, Xiaoping An, Yang Jia, Jingwei Qi and Yuan Wang
Foods 2025, 14(4), 688; https://doi.org/10.3390/foods14040688 - 17 Feb 2025
Cited by 1 | Viewed by 893
Abstract
Dietary regulation of intramuscular fat (IMF) deposition and fatty acid composition offers an effective strategy to enhance meat nutritional value. As phytogenic supplements rich in bioactive compounds, complex plant extracts (CPE) have demonstrated potential in improving meat quality through lipid metabolism modulation while [...] Read more.
Dietary regulation of intramuscular fat (IMF) deposition and fatty acid composition offers an effective strategy to enhance meat nutritional value. As phytogenic supplements rich in bioactive compounds, complex plant extracts (CPE) have demonstrated potential in improving meat quality through lipid metabolism modulation while ensuring food safety. In this study, we used 36 female sheep, approximately 4 months old and with a similar weight (29.92 ± 2.52 kg), to investigate the effects of CPE supplementation (80 mg/kg) on lipid metabolism. After the 75-day standardized feeding trial, the sheep were subjected to humane slaughter procedures and collected the Longissimus dorsi muscle (LDM) for further experimental process. The findings indicate that CPE significantly increased (p < 0.05) the IMF content (36%) and total fatty acids concentration (10,045.79 to 26,451.99 ug/g). Lipid metabolism in LDM was mainly affected by regulating phospholipids (six lipid subclasses were affected). The qRT-PCR analysis showed that differential expressed genes, PLA2G2D and PLA2G4E, associated with lipid metabolism were significantly reduced. CPE appears to modulate the fatty acids through sphingolipid, linolenic acid metabolism, and glycosphingolipid biosynthesis pathways. Thus, this study uncoded the mechanisms of CPE on fatty acid, providing critical evidence that CPE can regulate the meat quality of ruminants. Full article
(This article belongs to the Section Foodomics)
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19 pages, 4850 KiB  
Article
Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle
by Ziyu Chen, Xiaoqian Wu, Dongbin Zheng, Yuling Wang, Jie Chai, Tinghuan Zhang, Pingxian Wu, Minghong Wei, Ting Zhou, Keren Long, Mingzhou Li, Long Jin and Li Chen
Cells 2025, 14(1), 37; https://doi.org/10.3390/cells14010037 - 2 Jan 2025
Cited by 2 | Viewed by 1840
Abstract
Porcine latissimus dorsi muscle (LDM) is a crucial source of pork products. Meat quality indicators, such as the proportion of muscle fibers and intramuscular fat (IMF) deposition, vary during the growth and development of pigs. Numerous studies have highlighted the heterogeneous nature of [...] Read more.
Porcine latissimus dorsi muscle (LDM) is a crucial source of pork products. Meat quality indicators, such as the proportion of muscle fibers and intramuscular fat (IMF) deposition, vary during the growth and development of pigs. Numerous studies have highlighted the heterogeneous nature of skeletal muscle, with phenotypic differences reflecting variations in cellular composition and transcriptional profiles. This study investigates the cellular-level transcriptional characteristics of LDM in large white pigs at two growth stages (170 days vs. 245 days) using single-nucleus RNA sequencing (snRNA-seq). We identified 56,072 cells across 12 clusters, including myofibers, fibro/adipogenic progenitor (FAP) cells, muscle satellite cells (MUSCs), and other resident cell types. The same cell types were present in the LDM at both growth stages, but their proportions and states differed. A higher proportion of FAPs was observed in the skeletal muscle of 245-day-old pigs. Additionally, these cells exhibited more active communication with other cell types compared to 170-day-old pigs. For instance, more interactions were found between FAPs and pericytes or endothelial cells in 245-day-old pigs, including collagen and integrin family signaling. Three subclasses of FAPs was identified, comprising FAPs_COL3A1+, FAPs_PDE4D+, and FAPs_EBF1+, while adipocytes were categorized into Ad_PDE4D+ and Ad_DGAT2+ subclasses. The proportions of these subclasses differed between the two age groups. We also constructed differentiation trajectories for FAPs and adipocytes, revealing that FAPs in 245-day-old pigs differentiated more toward fibrosis, a characteristic reminiscent of the high prevalence of skeletal muscle fibrosis in aging humans. Furthermore, the Ad_PDE4D+ adipocyte subclass, predominant in 245-day-old pigs, originated from FAPs_PDE4D+ expressing the same gene, while the Ad_DGAT2+ subclass stemmed from FAPs_EBF1+. In conclusion, our study elucidates transcriptional differences in skeletal muscle between two growth stages of pigs and provides insights into mechanisms relevant to pork meat quality and skeletal muscle diseases. Full article
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