1
|
Zhao Y, Chen S, Yuan J, Shi Y, Wang Y, Xi Y, Qi X, Guo Y, Sheng X, Liu J, Zhou L, Wang C, Xing K. Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network for Intramuscular Fat in Pigs. Genes (Basel) 2023; 14:168. [PMID: 36672909 PMCID: PMC9859044 DOI: 10.3390/genes14010168] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Intramuscular fat (IMF) is an essential trait closely related to meat quality. The IMF trait is a complex quantitative trait that is regulated by multiple genes. In order to better understand the process of IMF and explore the key factors affecting IMF deposition, we identified differentially expressed mRNA, miRNA, and lncRNA in the longissimus dorsi muscle (LD) between Songliao Black (SL) pigs and Landrace pigs. We obtained 606 differentially expressed genes (DEGs), 55 differentially expressed miRNAs (DEMs), and 30 differentially expressed lncRNAs (DELs) between the SL pig and Landrace pig. Enrichment results from GO and KEGG indicate that DEGs are involved in fatty acid metabolism and some pathways related to glycogen synthesis. We constructed an lncRNA-miRNA-mRNA interaction network with 18 DELs, 11 DEMs, and 42 DEGs. Finally, the research suggests that ARID5B, CPT1B, ACSL1, LPIN1, HSP90AA1, IRS1, IRS2, PIK3CA, PIK3CB, and PLIN2 may be the key genes affecting IMF deposition. The LncRNAs MSTRG.19948.1, MSTRG.13120.1, MSTRG.20210.1, and MSTRG.10023.1, and the miRNAs ssc-miRNA-429 and ssc-miRNA-7-1, may play a regulatory role in IMF deposition through their respective target genes. Our research provides a reference for further understanding the regulatory mechanism of IMF.
Collapse
Affiliation(s)
- Yanhui Zhao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Shaokang Chen
- Beijing Animal Husbandry Station, Beijing 100101, China
| | - Jiani Yuan
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yumei Shi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yan Wang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yufei Xi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Xiaolong Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Xihui Sheng
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lei Zhou
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chuduan Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| |
Collapse
|
2
|
Muñoz M, Bozzi R, García-Casco J, Núñez Y, Ribani A, Franci O, García F, Škrlep M, Schiavo G, Bovo S, Utzeri VJ, Charneca R, Martins JM, Quintanilla R, Tibau J, Margeta V, Djurkin-Kušec I, Mercat MJ, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fernández AI, Fontanesi L, Óvilo C. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Sci Rep 2019; 9:13546. [PMID: 31537860 PMCID: PMC6753209 DOI: 10.1038/s41598-019-49830-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/30/2019] [Indexed: 11/27/2022] Open
Abstract
Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.
Collapse
Affiliation(s)
- M Muñoz
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - R Bozzi
- DAGRI, Animal Science Section, Università degli Studi di Firenze, Firenze, Italy
| | - J García-Casco
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - A Ribani
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - O Franci
- DAGRI, Animal Science Section, Università degli Studi di Firenze, Firenze, Italy
| | - F García
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - M Škrlep
- Kmetijski inštitut Slovenije, Hacquetova ulica 17, SI-1000, Ljubljana, Slovenia
| | - G Schiavo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - S Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - V J Utzeri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - R Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - J M Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - R Quintanilla
- IRTA, Programa de Genética y Mejora Animal, Barcelona, Spain
| | - J Tibau
- IRTA, Programa de Genética y Mejora Animal, Barcelona, Spain
| | - V Margeta
- Faculty of Agrobiotechnical Sciences Osijek, University of Osijek, Osijek, Croatia
| | - I Djurkin-Kušec
- Faculty of Agrobiotechnical Sciences Osijek, University of Osijek, Osijek, Croatia
| | - M J Mercat
- IFIP - Institut du Porc, Le Rheu, France
| | - J Riquet
- INRA, Génétique Physiologie et Système d'Elevage, Castanet-Tolosan, France
| | - J Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - C Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Wolpertshausen, Germany
| | - V Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - J P Araujo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Ponte de Lima, Portugal
| | - Č Radović
- Institute for Animal Husbandry-Pig Research Department, Autoput for Zagreb 16, 11080, Belgrade-Zemun, Serbia
| | - R Savić
- University of Belgrade, Faculty of agriculture, Nemanjina 6, 11080, Belgrade-Zemun, Serbia
| | - D Karolyi
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb, Croatia
| | - M Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Roma, Italy
| | - M Čandek-Potokar
- Kmetijski inštitut Slovenije, Hacquetova ulica 17, SI-1000, Ljubljana, Slovenia
| | - A I Fernández
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - L Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - C Óvilo
- Departamento Mejora Genética Animal, INIA, Madrid, Spain.
| |
Collapse
|
3
|
Dalrymple BP, Guo B. TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Intramuscular fat deposition in ruminants and pigs: A transcriptomics perspective. J Anim Sci 2017; 95:2272-2283. [PMID: 28727003 DOI: 10.2527/jas.2016.1112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The genomics era has led to an explosion in the study of gene expression in production animals. Intramuscular fat (IMF) content (both high and low) and composition are major quality attributes of meat, and more than 90 transcriptomic studies of IMF deposition have been undertaken in the ruminants and pigs since 2001, with the majority since 2008. The studies have implicated many genes involved in the control of adipogenesis, lipogenesis, and deposition of IMF, but there is relatively little consistency between the different studies. However, the genes encoding the synthesis enzymes acetyl-CoA carboxylase α, fatty acid synthase, and stearoyl-CoA desaturase; the fatty acid binding protein 4; the potential signaling protein thyroid hormone responsive; and the regulators C/EBPα, PPARγ, and sterol regulatory element binding transcription factor 1 are supported by 5 or more of the 90 studies. By combining the results of all the studies, complete pathways for long-chain fatty acid (LCFA) and triacylglyceride (TAG) synthesis are identified, as are a number of genes encoding proteins probably associated with the storage of TAG and genes encoding a number of known and potential adipokines. In contrast, support for the association of lipolytic pathways with IMF percentage is less strong. Differences in experimental design-in particular, the age of the animals, the rate of IMF deposition at sampling, the past nutritional history of the animals used, and the complexities of using a tissue with mixed cell types-have contributed to the differences in results and interpretation. Biomarkers predictive of future IMF percentage, facilitating reaching optimal IMF content at slaughter, may have industry utility, but to be useful in animal biopsy and postslaughter samples, where multiple cell types are present, genes must be carefully chosen to ensure that they are informative about the expected processes. Despite these problems, candidate biomarkers for estimation of de novo intramuscular adipocyte LCFA synthesis, LCFA uptake rate by intramuscular adipocytes, and IMF deposition rate have been identified and examples of their utility have been published. However, further work is required to demonstrate how best to apply the assays for the benefit of the relevant livestock production industries.
Collapse
|
5
|
Hausman GJ, Basu U, Du M, Fernyhough-Culver M, Dodson MV. Intermuscular and intramuscular adipose tissues: Bad vs. good adipose tissues. Adipocyte 2014; 3:242-55. [PMID: 26317048 DOI: 10.4161/adip.28546] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 12/23/2022] Open
Abstract
Human studies of the influence of aging and other factors on intermuscular fat (INTMF) were reviewed. Intermuscular fat increased with weight loss, weight gain, or with no weight change with age in humans. An increase in INTMF represents a similar threat to type 2 diabetes and insulin resistance as does visceral adipose tissue (VAT). Studies of INTMF in animals covered topics such as quantitative deposition and genetic relationships with other fat depots. The relationship between leanness and higher proportions of INTMF fat in pigs was not observed in human studies and was not corroborated by other pig studies. In humans, changes in muscle mass, strength and quality are associated with INTMF accretion with aging. Gene expression profiling and intrinsic methylation differences in pigs demonstrated that INTMF and VAT are primarily associated with inflammatory and immune processes. It seems that in the pig and humans, INTMF and VAT share a similar pattern of distribution and a similar association of components dictating insulin sensitivity. Studies on intramuscular (IM) adipocyte development in meat animals were reviewed. Gene expression analysis and genetic analysis have identified candidate genes involved in IM adipocyte development. Intramuscular (IM) adipocyte development in human muscle is only seen during aging and some pathological circumstance. Several genetic links between human and meat animal adipogenesis have been identified. In pigs, the Lipin1 and Lipin 2 gene have strong genetic effects on IM accumulation. Lipin1 deficiency results in immature adipocyte development in human lipodystrophy. In humans, overexpression of Perilipin 2 (PLIN2) facilitates intramyocellular lipid accretion whereas in pigs PLIN2 gene expression is associated with IM deposition. Lipins and perilipins may influence intramuscular lipid regardless of species.
Collapse
|
6
|
Lipins, lipinopathies, and the modulation of cellular lipid storage and signaling. Prog Lipid Res 2013; 52:305-16. [PMID: 23603613 DOI: 10.1016/j.plipres.2013.04.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 03/29/2013] [Accepted: 04/04/2013] [Indexed: 01/13/2023]
Abstract
Members of the lipin protein family are phosphatidate phosphatase (PAP) enzymes, which catalyze the dephosphorylation of phosphatidic acid to diacylglycerol, the penultimate step in TAG synthesis. Lipins are unique among the glycerolipid biosynthetic enzymes in that they also promote fatty acid oxidation through their activity as co-regulators of gene expression by DNA-bound transcription factors. Lipin function has been evolutionarily conserved from a single ortholog in yeast to the mammalian family of three lipin proteins-lipin-1, lipin-2, and lipin-3. In mice and humans, the levels of lipin activity are a determinant of TAG storage in diverse cell types, and humans with deficiency in lipin-1 or lipin-2 have severe metabolic diseases. Recent work has highlighted the complex physiological interactions between members of the lipin protein family, which exhibit both overlapping and unique functions in specific tissues. The analysis of "lipinopathies" in mouse models and in humans has revealed an important role for lipin activity in the regulation of lipid intermediates (phosphatidate and diacylglycerol), which influence fundamental cellular processes including adipocyte and nerve cell differentiation, adipocyte lipolysis, and hepatic insulin signaling. The elucidation of lipin molecular and physiological functions could lead to novel approaches to modulate cellular lipid storage and metabolic disease.
Collapse
|