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Pareek CS, Sachajko M, Kalra G, Sultana S, Szostak A, Chalaskiewicz K, Kepka-Borkowska K, Poławska E, Ogłuszka M, Pierzchała D, Starzyński R, Taniguchi H, Juszczuk-Kubiak E, Lepczyński A, Ślaska B, Kozera W, Czarnik U, Wysocki P, Kadarmideen HN, Te Pas MFW, Szyda J, Pierzchała M. Identification of trait-associated microRNA modules in liver transcriptome of pig fed with PUFAs-enriched supplementary diet. J Appl Genet 2024:10.1007/s13353-024-00912-w. [PMID: 39546271 DOI: 10.1007/s13353-024-00912-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 08/16/2024] [Accepted: 10/11/2024] [Indexed: 11/17/2024]
Abstract
Dietary lipids provide energy, are cellular structural components, and are involved in physiological processes. Lipids are the dietary source in supplementary diet experiments in pigs. This study aims to investigate the dietary effects of PUFAs on the hepatic transcriptome and physiological pathways of two diets on two pig breeds. Polish Landrace (PL: n = 6) and six PLxDuroc (PLxD: n = 6) pigs were fed with a normal diet (n = 3) or PUFAs-enriched healthy diet (n = 3), and the hepatic miRNA profiles were studied for weighted gene co-expression network analysis biological interactions between gene networks and metabolic pathways of DE miRNA genes. The study identified trait-associated modules that were significantly associated with four phenotypic traits in the dietary groups of PL and PLxD: meat colour (a*), shoulder subcutaneous fat thickness, conductivity 24 h post-mortem (PE24), and ashes. Trait-wise, a large set of co-expressed miRNAs of porcine liver were identified in these trait-associated significant modules (9, 7, 2, and 8) in PL and PLxD. Each module is represented by a module eigengene (ME). Forty-four miRNAs out of 94 miRNAs interacted with 6719 statistically significant target genes with a target score > 90. The GO/pathway analysis showed association with pathways including regulation of metallopeptidase activity, sebaceous gland development, collagen fibril organization, WNT signalling, epithelial tube morphogenesis, etc. The study showed the differences in miRNA expression between the dietary groups of PL and PLxD breeds. Hub genes of discovered miRNA clusters can be considered predicted miRNA genes associated with PE24, meat colour, shoulder subcutaneous fat thickness, and ashes. Discovered target genes for miRNA clusters play significant roles in biological functions such as (i) muscle and body growth development, (ii) different cellular processes and developments, (iii) system development, and (iv) metabolic processes.
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Affiliation(s)
- C S Pareek
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Toruń, Poland
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - M Sachajko
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Toruń, Poland
| | - G Kalra
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Toruń, Poland
| | - S Sultana
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100, Toruń, Poland
| | - A Szostak
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland
| | - K Chalaskiewicz
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland
| | - K Kepka-Borkowska
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland
| | - E Poławska
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland
| | - M Ogłuszka
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland
| | - D Pierzchała
- Maria Sklodowska-Curie National Research Institute of Oncology, W.K. Roentgena 5 Str, 02-781, Warsaw, Poland
| | - R Starzyński
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland
| | - H Taniguchi
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland
- African Genome Center, Mohammed VI Polytechnic University, UM6P, Lot 660, Hay Moulay Rachid Ben Guerir, 43150, Morocco
| | - E Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology Prof. Wacław, Dąbrowski Institute of Agriculture and Food Biotechnology - State Research Institute (IBPRS-PIB), Rakowiecka 36 Str, 02-532, Warsaw, Poland
| | - A Lepczyński
- Department of Physiology, Cytobiology and Proteomics, West Pomeranian University of Technology, K. Janickiego 32 Str, 71-270, Szczecin, Poland
| | - B Ślaska
- Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13 Str, 20-950, Lublin, Poland
| | - W Kozera
- Department of Pig Breeding, Department of Animal Biochemistry and Biotechnology, Faculty of Animal Bio-Engineering, University of Warmia and Mazury in Olsztyn, Ul. M. Oczapowskiego 5 Str, 10-719, Olsztyn, Poland
| | - U Czarnik
- Department of Pig Breeding, Department of Animal Biochemistry and Biotechnology, Faculty of Animal Bio-Engineering, University of Warmia and Mazury in Olsztyn, Ul. M. Oczapowskiego 5 Str, 10-719, Olsztyn, Poland
| | - P Wysocki
- Department of Pig Breeding, Department of Animal Biochemistry and Biotechnology, Faculty of Animal Bio-Engineering, University of Warmia and Mazury in Olsztyn, Ul. M. Oczapowskiego 5 Str, 10-719, Olsztyn, Poland
| | - H N Kadarmideen
- Department of Animal and Veterinary Sciences, Aarhus University, Blichers Alle 20, 8830, Tjele, Denmark
| | - M F W Te Pas
- Wageningen Livestock Research, Wageningen University and Research, 6708 WD, Wageningen, The Netherlands
| | - J Szyda
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wrocław, Poland
| | - M Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Ul. Postepu 36A Str, 05-552, Jastrzebiec, Magdalenka, Poland.
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Lv J, Yang F, Li Y, Gao N, Zeng Q, Ma H, He J, Zhang Y. Characterization and Function Analysis of miRNA Editing during Fat Deposition in Chinese Indigenous Ningxiang Pigs. Vet Sci 2024; 11:183. [PMID: 38668450 PMCID: PMC11054885 DOI: 10.3390/vetsci11040183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
This study aimed to identify active miRNA editing sites during adipose development in Ningxiang pigs and analyze their characteristics and functions. Based on small RNA-seq data from the subcutaneous adipose tissues of Ningxiang pigs at four stages-30 days (piglet), 90 days (nursery), 150 days (early fattening), and 210 days (late fattening)-we constructed a developmental map of miRNA editing in the adipose tissues of Ningxiang pigs. A total of 505 miRNA editing sites were identified using the revised pipeline, with C-to-U editing types being the most prevalent, followed by U-to-C, A-to-G, and G-to-U. Importantly, these four types of miRNA editing exhibited base preferences. The number of editing sites showed obvious differences among age groups, with the highest occurrence of miRNA editing events observed at 90 days of age and the lowest at 150 days of age. A total of nine miRNA editing sites were identified in the miRNA seed region, with significant differences in editing levels (p < 0.05) located in ssc-miR-23a, ssc-miR-27a, ssc-miR-30b-5p, ssc-miR-15a, ssc-miR-497, ssc-miR-15b, and ssc-miR-425-5p, respectively. Target gene prediction and KEGG enrichment analyses indicated that the editing of miR-497 might potentially regulate fat deposition by inhibiting adipose synthesis via influencing target binding. These results provide new insights into the regulatory mechanism of pig fat deposition.
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Affiliation(s)
- Jiayu Lv
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Yiyang Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.L.); (F.Y.); (Y.L.); (N.G.); (Q.Z.); (H.M.)
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Changsha 410000, China
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Hou J, Ji X, Chu X, Wang B, Sun K, Wei H, Zhang Y, Song Z, Wen F. Mulberry Leaf Dietary Supplementation Can Improve the Lipo-Nutritional Quality of Pork and Regulate Gut Microbiota in Pigs: A Comprehensive Multi-Omics Analysis. Animals (Basel) 2024; 14:1233. [PMID: 38672381 PMCID: PMC11047539 DOI: 10.3390/ani14081233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Mulberry leaves, a common traditional Chinese medicine, represent a potential nutritional strategy to improve the fat profile, also known as the lipo-nutrition, of pork. However, the effects of mulberry leaves on pork lipo-nutrition and the microorganisms and metabolites in the porcine gut remain unclear. In this study, multi-omics analysis was employed in a Yuxi black pig animal model to explore the possible regulatory mechanism of mulberry leaves on pork quality. Sixty Yuxi black pigs were divided into two groups: the control group (n = 15) was fed a standard diet, and the experimental group (n = 45) was fed a diet supplemented with 8% mulberry leaves. Experiments were performed in three replicates (n = 15 per replicate); the two diets were ensured to be nutritionally balanced, and the feeding period was 120 days. The results showed that pigs receiving the diet supplemented with mulberry leaves had significantly reduced backfat thickness (p < 0.05) and increased intramuscular fat (IMF) content (p < 0.05) compared with pigs receiving the standard diet. Lipidomics analysis showed that mulberry leaves improved the lipid profile composition and increased the proportion of triglycerides (TGs). Interestingly, the IMF content was positively correlated with acyl C18:2 and negatively correlated with C18:1 of differential TGs. In addition, the cecal microbiological analysis showed that mulberry leaves could increase the abundance of bacteria such as UCG-005, Muribaculaceae_norank, Prevotellaceae_NK3B31_group, and Limosilactobacillus. Simultaneously, the relative levels of L-tyrosine-ethyl ester, oleic acid methyl ester, 21-deoxycortisol, N-acetyldihydrosphingosine, and mulberrin were increased. Furthermore, we found that mulberry leaf supplementation significantly increased the mRNA expression of lipoprotein lipase, fatty acid-binding protein 4, and peroxisome proliferators-activated receptor γ in muscle (p < 0.01). Mulberry leaf supplementation significantly increased the mRNA expression of diacylglycerol acyltransferase 1 (p < 0.05) while significantly decreasing the expression of acetyl CoA carboxylase in backfat (p < 0.05). Furthermore, mulberry leaf supplementation significantly upregulated the mRNA expression of hormone-sensitive triglyceride lipase and peroxisome proliferator-activated receptor α (p < 0.05) in backfat. In addition, mulberry leaf supplementation led to increased serum leptin and adiponectin (p < 0.01). Collectively, this omic profile is consistent with an increased ratio of IMF to backfat in the pig model.
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Affiliation(s)
- Junjie Hou
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
| | - Xiang Ji
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
| | - Xiaoran Chu
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
| | - Binjie Wang
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
| | - Kangle Sun
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
| | - Haibo Wei
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
| | - Yu Zhang
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
| | - Zhen Song
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
- The Kay Laboratory of High Quality Livestock and Poultry Germplasm Resources and Genetic Breeding of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Fengyun Wen
- College of Animal Scienceand Technology, Henan University of Science and Technology, Luoyang 471003, China; (J.H.)
- The Kay Laboratory of High Quality Livestock and Poultry Germplasm Resources and Genetic Breeding of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
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Zhang W, Zhao T, Gao X, Ma S, Gong T, Yang Y, Li M, Cao G, Guo X, Li B. miR-10a-5p Regulates the Proliferation and Differentiation of Porcine Preadipocytes Targeting the KLF11 Gene. Animals (Basel) 2024; 14:337. [PMID: 38275797 PMCID: PMC10812476 DOI: 10.3390/ani14020337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
In the swine industry, meat quality, color, and texture are influenced by the excessive differentiation of fat cells. miRNAs have emerged as integral regulators of adipose development. This study delves into the influence of miR-10a-5b on the proliferation and differentiation of pig preadipocytes. Our findings reveal that miR-10a-5b is prevalent across various tissues. It hinders preadipocyte proliferation, amplifies the expression of adipogenic genes, promotes lipid accumulation, and, as a result, advances preadipocyte differentiation. We predict that KLF11 is the target gene of miRNA. A dual-fluorescence reporter assay was conducted to validate the binding sites of miR-10a-5b on the 3'UTR of the KLF11 mRNA. Results showed that miR-10a-5b targeted KLF11 3'UTR and reduced the fluorescence activity of the dual-fluorescent reporter vector. Our research also indicates that miR-10a-5b targets and downregulates the expression of both mRNA and the protein levels of KLF11. During the differentiation of the preadipocytes, KLF11 inhibited adipose differentiation and was able to suppress the promotion of adipose differentiation by miR-10a-5b. This underscores miR-10a-5b's potential as a significant regulator of preadipocyte behavior by modulating KLF11 expression, offering insights into the role of functional miRNAs in fat deposition.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.Z.); (T.Z.); (X.G.); (S.M.); (T.G.); (Y.Y.); (M.L.); (G.C.)
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (W.Z.); (T.Z.); (X.G.); (S.M.); (T.G.); (Y.Y.); (M.L.); (G.C.)
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