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Freitas FAO, Brito LF, Fanalli SL, Gonçales JL, da Silva BPM, Durval MC, Ciconello FN, de Oliveira CS, Nascimento LE, Gervásio IC, Gomes JD, Moreira GCM, Silva-Vignato B, Coutinho LL, de Almeida VV, Cesar ASM. Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs. BMC Genomics 2024; 25:14. [PMID: 38166730 PMCID: PMC10759680 DOI: 10.1186/s12864-023-09863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs. RESULTS The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the "Meat and Carcass" type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes. CONCLUSIONS After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone.
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Affiliation(s)
- Felipe André Oliveira Freitas
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Janaína Lustosa Gonçales
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | - Mariah Castro Durval
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Fernanda Nery Ciconello
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | | | - Izally Carvalho Gervásio
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | - Julia Dezen Gomes
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | - Bárbara Silva-Vignato
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | - Vivian Vezzoni de Almeida
- College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia, 74001-970, GO, Brazil
| | - Aline Silva Mello Cesar
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil.
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil.
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São José GLF, Nuñez AJC, Gomes JD, Schinckel AP, Cesar ASM, Luchiari Filho A, do Carmo AS, Brito LF, de Almeida VV. Production and meat quality traits of genetically lean immunocastrated pigs naturally divergent for loin tenderness. Trop Anim Health Prod 2023; 56:22. [PMID: 38123841 DOI: 10.1007/s11250-023-03875-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Warner-Bratzler Shear Force (WBSF) is a quantitative measurement of meat toughness that has great impact on the consumer acceptability of meat. This study was conducted to evaluate growth performance, carcass and meat quality characteristics, and fatty acids profile of longissimus lumborum (LL) intramuscular fat (IMF) of pigs that are genetically divergent for WBSF. Based on WBSF values of the LL from a previous study, 12 immunocastrated male pigs selected from 96 pigs were divided into two groups with high WBSF (53.28 to 42.50 N) and low WBSF (37.27 to 27.79 N). Although high-WBSF pigs tended to have improved (P = 0.08) gain-to-feed ratio, overall performance was similar between WBSF groups. High-WBSF pigs also tended to have higher (P = 0.09) cooling loss and lean percentage as well as decreased (P = 0.08) 10th-rib backfat depth than low-WBSF pigs. Loins from high-WBSF pigs tended to have lower (P = 0.07) IMF content and higher (P = 0.09) cooking loss than low-WBSF pigs. Compared to low-WBSF pigs, IMF of the LL from high-WBSF pigs had lower (P = 0.05) percentage of oleic acid and tended to have a decreased (P = 0.07) percentage of total monounsaturated fatty acids. Loins from pigs with high WBSF tended to have increased (P = 0.09) total polyunsaturated fatty acids (PUFA) content and had higher (P = 0.03) PUFA: saturated fatty acid ratio than low-WBSF pigs. Selecting pigs for pork tenderness could potentially conflict with lean growth efficiency and a healthier fatty acids profile for human consumption.
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Affiliation(s)
| | | | - Julia Dezen Gomes
- Department of Agri-Food Industry, Food, and Nutrition, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Aline Silva Mello Cesar
- Department of Agri-Food Industry, Food, and Nutrition, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Albino Luchiari Filho
- Department of Agri-Food Industry, Food, and Nutrition, University of São Paulo, Piracicaba, São Paulo, Brazil
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da Silva BPM, Fanalli SL, Gomes JD, de Almeida VV, Fukumasu H, Freitas FAO, Moreira GCM, Silva-Vignato B, Reecy JM, Koltes JE, Koltes D, de Carvalho Balieiro JC, de Alencar SM, da Silva JPM, Coutinho LL, Afonso J, Regitano LCDA, Mourão GB, Luchiari Filho A, Cesar ASM. Brain fatty acid and transcriptome profiles of pig fed diets with different levels of soybean oil. BMC Genomics 2023; 24:91. [PMID: 36855067 PMCID: PMC9976441 DOI: 10.1186/s12864-023-09188-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND The high similarity in anatomical and neurophysiological processes between pigs and humans make pigs an excellent model for metabolic diseases and neurological disorders. Lipids are essential for brain structure and function, and the polyunsaturated fatty acids (PUFA) have anti-inflammatory and positive effects against cognitive dysfunction in neurodegenerative diseases. Nutrigenomics studies involving pigs and fatty acids (FA) may help us in better understanding important biological processes. In this study, the main goal was to evaluate the effect of different levels of dietary soybean oil on the lipid profile and transcriptome in pigs' brain tissue. RESULTS Thirty-six male Large White pigs were used in a 98-day study using two experimental diets corn-soybean meal diet containing 1.5% soybean oil (SOY1.5) and corn-soybean meal diet containing 3.0% soybean oil (SOY3.0). No differences were found for the brain total lipid content and FA profile between the different levels of soybean oil. For differential expression analysis, using the DESeq2 statistical package, a total of 34 differentially expressed genes (DEG, FDR-corrected p-value < 0.05) were identified. Of these 34 DEG, 25 are known-genes, of which 11 were up-regulated (log2 fold change ranging from + 0.25 to + 2.93) and 14 were down-regulated (log2 fold change ranging from - 3.43 to -0.36) for the SOY1.5 group compared to SOY3.0. For the functional enrichment analysis performed using MetaCore with the 34 DEG, four pathway maps were identified (p-value < 0.05), related to the ALOX15B (log2 fold change - 1.489), CALB1 (log2 fold change - 3.431) and CAST (log2 fold change + 0.421) genes. A "calcium transport" network (p-value = 2.303e-2), related to the CAST and CALB1 genes, was also identified. CONCLUSION The results found in this study contribute to understanding the pathways and networks associated with processes involved in intracellular calcium, lipid metabolism, and oxidative processes in the brain tissue. Moreover, these results may help a better comprehension of the modulating effects of soybean oil and its FA composition on processes and diseases affecting the brain tissue.
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Affiliation(s)
- Bruna Pereira Martins da Silva
- grid.11899.380000 0004 1937 0722Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Simara Larissa Fanalli
- grid.11899.380000 0004 1937 0722Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Julia Dezen Gomes
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Vivian Vezzoni de Almeida
- grid.411195.90000 0001 2192 5801College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia, Goiás Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Felipe André Oliveira Freitas
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Bárbara Silva-Vignato
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - James Mark Reecy
- grid.34421.300000 0004 1936 7312College of Agriculture and Life Sciences, Iowa State University, Ames, IA USA
| | - James Eugene Koltes
- grid.34421.300000 0004 1936 7312College of Agriculture and Life Sciences, Iowa State University, Ames, IA USA
| | - Dawn Koltes
- grid.34421.300000 0004 1936 7312College of Agriculture and Life Sciences, Iowa State University, Ames, IA USA
| | - Júlio Cesar de Carvalho Balieiro
- grid.11899.380000 0004 1937 0722School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Severino Matias de Alencar
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Julia Pereira Martins da Silva
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Juliana Afonso
- grid.460200.00000 0004 0541 873XEmbrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | | | - Gerson Barreto Mourão
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Albino Luchiari Filho
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Aline Silva Mello Cesar
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil. .,Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil.
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Fanalli SL, da Silva BPM, Gomes JD, Durval MC, de Almeida VV, Moreira GCM, Silva-Vignato B, Afonso J, Freitas FAO, Reecy JM, Koltes JE, Koltes D, Garrick D, Correia de Almeida Regitano L, Balieiro JCDC, Mourão GB, Coutinho LL, Fukumasu H, de Alencar SM, Luchiari Filho A, Cesar ASM. RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids. Front Genet 2023; 14:1053021. [PMID: 36816031 PMCID: PMC9936315 DOI: 10.3389/fgene.2023.1053021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Pigs (Sus scrofa) are an animal model for metabolic diseases in humans. Pork is an important source of fatty acids (FAs) in the human diet, as it is one of the most consumed meats worldwide. The effects of dietary inclusion of oils such as canola, fish, and soybean oils on pig gene expression are mostly unknown. Our objective was to evaluate FA composition, identify changes in gene expression in the liver of male pigs fed diets enriched with different FA profiles, and identify impacted metabolic pathways and gene networks to enlighten the biological mechanisms' variation. Large White male pigs were randomly allocated to one of three diets with 18 pigs in each; all diets comprised a base of corn and soybean meal to which either 3% of soybean oil (SOY), 3% canola oil (CO), or 3% fish oil (FO) was added for a 98-day trial during the growing and finishing phases. RNA sequencing was performed on the liver samples of each animal by Illumina technology for differential gene expression analyses, using the R package DESeq2. The diets modified the FA profile, mainly in relation to polyunsaturated and saturated FAs. Comparing SOY vs. FO, 143 differentially expressed genes (DEGs) were identified as being associated with metabolism, metabolic and neurodegenerative disease pathways, inflammatory processes, and immune response networks. Comparing CO vs. SOY, 148 DEGs were identified, with pathways related to FA oxidation, regulation of lipid metabolism, and metabolic and neurodegenerative diseases. Our results help explain the behavior of genes with differential expression in metabolic pathways resulting from feeding different types of oils in pig diets.
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Affiliation(s)
- Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil
| | | | - Julia Dezen Gomes
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Mariah Castro Durval
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil
| | | | | | - Bárbara Silva-Vignato
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | | | - Felipe André Oliveira Freitas
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - James Mark Reecy
- Animal Science Department, Iowa State University, Ames, IA, United States
| | | | - Dawn Koltes
- Animal Science Department, Iowa State University, Ames, IA, United States
| | - Dorian Garrick
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, New Zealand
| | | | | | - Gerson Barreto Mourão
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Heidge Fukumasu
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil
| | - Severino Matias de Alencar
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Albino Luchiari Filho
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil,Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil,*Correspondence: Aline Silva Mello Cesar,
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5
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Fanalli SL, da Silva BPM, Gomes JD, de Almeida VV, Freitas FAO, Moreira GCM, Silva-Vignato B, Afonso J, Reecy J, Koltes J, Koltes D, de Almeida Regitano LC, Garrick DJ, de Carvalho Balieiro JC, Meira AN, Freitas L, Coutinho LL, Fukumasu H, Mourão GB, de Alencar SM, Luchiari Filho A, Cesar ASM. Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs. Animals (Basel) 2022; 12:ani12131632. [PMID: 35804531 PMCID: PMC9265114 DOI: 10.3390/ani12131632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Findings from the analysis of the pig transcriptome may help to better understand the biological mechanisms that can be modulated by the diet. Thus, the aim of this study was to identify the differentially expressed genes from the skeletal muscle and liver samples of pigs fed diets with two different levels of soybean oil (1.5 or 3%). The FA profile in the tissues was modified by the diet mainly related to monounsaturated (MUFA) and polyunsaturated (PUFA). This nutrigenomics study verified the effect of different levels of soybean oil in the pig diet on the transcriptome profile of skeletal muscle and liver, where the higher level of soybean oil added to the diet led to a higher expression of genes targeting biological processes related to lipid oxidation and consequently to metabolic diseases and inflammation. Abstract The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.
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Affiliation(s)
- Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
| | - Bruna Pereira Martins da Silva
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
| | - Julia Dezen Gomes
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Vivian Vezzoni de Almeida
- College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia 74690-900, GO, Brazil;
| | - Felipe André Oliveira Freitas
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | | | - Bárbara Silva-Vignato
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 70770-901, SP, Brazil; (J.A.); (L.C.d.A.R.)
| | - James Reecy
- College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA; (J.R.); (J.K.); (D.K.)
| | - James Koltes
- College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA; (J.R.); (J.K.); (D.K.)
| | - Dawn Koltes
- College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA; (J.R.); (J.K.); (D.K.)
| | | | - Dorian John Garrick
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton 3214, New Zealand;
| | | | - Ariana Nascimento Meira
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Luciana Freitas
- DB Genética de Suínos, Patos de Minas 38706-000, MG, Brazil;
| | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Heidge Fukumasu
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
| | - Gerson Barreto Mourão
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Severino Matias de Alencar
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Albino Luchiari Filho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Aline Silva Mello Cesar
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
- Correspondence:
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6
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Fanalli SL, da Silva BPM, Gomes JD, Ciconello FN, de Almeida VV, Freitas FAO, Moreira GCM, Silva-Vignato B, Afonso J, Reecy J, Koltes J, Koltes D, Regitano LCA, de Carvalho Baileiro JC, Freitas L, Coutinho LL, Fukumasu H, de Alencar SM, Luchiari Filho A, Cesar ASM. Effect of dietary soybean oil inclusion on liver-related transcription factors in a pig model for metabolic diseases. Sci Rep 2022; 12:10318. [PMID: 35725871 PMCID: PMC9209463 DOI: 10.1038/s41598-022-14069-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/31/2022] [Indexed: 12/21/2022] Open
Abstract
Dietary fatty acids (FA) are components of the lipids, which contribute to membrane structure, energy input, and biological functions related to cellular signaling and transcriptome regulation. However, the consumers still associate dietary FA with fat deposition and increased occurrence of metabolic diseases such as obesity and atherosclerosis. Previous studies already demonstrated that some fatty acids are linked with inflammatory response, preventing metabolic diseases. To better understand the role of dietary FA on metabolic diseases, for the first time, a study to identify key transcription factors (TF) involved in lipid metabolism and inflammatory response by transcriptome analysis from liver samples of animal models was performed. The key TF were identified by functional enrichment analysis from the list of differentially expressed genes identified in liver samples between 35 pigs fed with 1.5% or 3.0% soybean oil. The functional enrichment analysis detected TF linked to lipid homeostasis and inflammatory response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key TF related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive food technology and science.
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Affiliation(s)
- Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, University of São Paulo, Campus Fernando Costa, Avenue Duque de Caxias Norte 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Bruna Pereira Martins da Silva
- Faculty of Animal Science and Food Engineering, University of São Paulo, Campus Fernando Costa, Avenue Duque de Caxias Norte 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Julia Dezen Gomes
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Fernanda Nery Ciconello
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Vivian Vezzoni de Almeida
- College of Veterinary Medicine and Animal Science, Federal University of Goiás, Nova Veneza, km 8, Campus Samambaia, Goiânia, Goiás, 74690-900, Brazil
| | - Felipe André Oliveira Freitas
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Gabriel Costa Monteiro Moreira
- University of Liège, GIGA Medical Genomics, Unit of Animal Genomics, Quartier Hôpital, Avenue de l'Hôpital, 11, 4000, Liège, Belgium
| | - Bárbara Silva-Vignato
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Juliana Afonso
- Embrapa Pecuária Sudeste, Km 234 s/nº, São Carlos, São Paulo, 13560-970, Brazil
| | - James Reecy
- Department of Animal Science, College of Agriculture and Life Sciences, Iowa State University, 1221, Kildee Hall, Ames, IA, 50011-3150, USA
| | - James Koltes
- Department of Animal Science, College of Agriculture and Life Sciences, Iowa State University, 1221, Kildee Hall, Ames, IA, 50011-3150, USA
| | - Dawn Koltes
- Department of Animal Science, College of Agriculture and Life Sciences, Iowa State University, 1221, Kildee Hall, Ames, IA, 50011-3150, USA
| | | | - Júlio Cesar de Carvalho Baileiro
- College of Veterinary Medicine and Animal Science, University of São Paulo, Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13.635-900, Brazil
| | - Luciana Freitas
- DB Genética de Suínos, Avenue Juscelino Kubitschek de Oliveira, 2094, Patos de Minas, MG, 38.706-000, Brazil
| | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Heidge Fukumasu
- Faculty of Animal Science and Food Engineering, University of São Paulo, Campus Fernando Costa, Avenue Duque de Caxias Norte 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Severino Matias de Alencar
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Albino Luchiari Filho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Aline Silva Mello Cesar
- Faculty of Animal Science and Food Engineering, University of São Paulo, Campus Fernando Costa, Avenue Duque de Caxias Norte 225, Pirassununga, São Paulo, 13635-900, Brazil. .,Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias 11, Piracicaba, São Paulo, 13418-900, Brazil.
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Yan H, Potu R, Lu H, Vezzoni de Almeida V, Stewart T, Ragland D, Armstrong A, Adeola O, Nakatsu CH, Ajuwon KM. Dietary fat content and fiber type modulate hind gut microbial community and metabolic markers in the pig. PLoS One 2013; 8:e59581. [PMID: 23573202 PMCID: PMC3616062 DOI: 10.1371/journal.pone.0059581] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/15/2013] [Indexed: 12/27/2022] Open
Abstract
Obesity leads to changes in the gut microbial community which contribute to the metabolic dysregulation in obesity. Dietary fat and fiber affect the caloric density of foods. The impact of dietary fat content and fiber type on the microbial community in the hind gut is unknown. Effect of dietary fat level and fiber type on hindgut microbiota and volatile fatty acid (VFA) profiles was investigated. Expression of metabolic marker genes in the gut, adipose tissue and liver was determined. A 2×2 experiment was conducted in pigs fed at two dietary fat levels (5% or 17.5% swine grease) and two fiber types (4% inulin, fermentable fructo-oligosaccharide or 4% solka floc, non-fermentable cellulose). High fat diets (HFD) resulted in a higher (P<0.05) total body weight gain, feed efficiency and back fat accumulation than the low fat diet. Feeding of inulin, but not solka floc, attenuated (P<0.05) the HFD-induced higher body weight gain and fat mass accumulation. Inulin feeding tended to lead to higher total VFA production in the cecum and resulted in a higher (P<0.05) expression of acyl coA oxidase (ACO), a marker of peroxisomal β-oxidation. Inulin feeding also resulted in lower expression of sterol regulatory element binding protein 1c (SREBP-1c), a marker of lipid anabolism. Bacteria community structure characterized by DGGE analysis of PCR amplified 16S rRNA gene fragments showed that inulin feeding resulted in greater bacterial population richness than solka floc feeding. Cluster analysis of pairwise Dice similarity comparisons of the DGGE profiles showed grouping by fiber type but not the level of dietary fat. Canonical correspondence analysis (CCA) of PCR- DGGE profiles showed that inulin feeding negatively correlated with back fat thickness. This study suggests a strong interplay between dietary fat level and fiber type in determining susceptibility to obesity.
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Affiliation(s)
- Hui Yan
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Ramesh Potu
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Hang Lu
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | | | - Terry Stewart
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Darryl Ragland
- Food Animal Production Medicine, School of Veterinary Medicine, Purdue University, Indiana, United States of America
| | - Arthur Armstrong
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Olayiwola Adeola
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Cindy H. Nakatsu
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Kolapo M. Ajuwon
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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8
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Sbardella M, Berenchtein B, de Andrade C, Perina DDP, de Almeida VV, Miyada VS. Rice oil as a soybean oil replacement in weanling pig diets. Livest Sci 2012. [DOI: 10.1016/j.livsci.2011.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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