Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

Simara Larissa Fanalli¹, Bruna Pereira Martins da Silva¹, Julia Dezen Gomes², Vivian Vezzoni de Almeida³, Felipe André Oliveira Freitas², Gabriel Costa Monteiro Moreira⁴, Bárbara Silva-Vignato², Juliana Afonso⁵, James Reecy⁶, James Koltes⁶, Dawn Koltes⁶, Luciana Correia de Almeida Regitano⁵, Dorian John Garrick⁷, Júlio Cesar de Carvalho Balieiro⁸, Ariana Nascimento Meira², Luciana Freitas⁹, Luiz Lehmann Coutinho², Heidge Fukumasu¹, Gerson Barreto Mourão², Severino Matias de Alencar², Albino Luchiari Filho², Aline Silva Mello Cesar^{1

2}

Affiliations

¹ Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil.
² Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil.
³ College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia 74690-900, GO, Brazil.
⁴ GIGA Medical Genomics, Unit of Animal Genomics, University of Liège, 4000 Liège, Belgium.
⁵ Embrapa Pecuária Sudeste, São Carlos 70770-901, SP, Brazil.
⁶ College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA.
⁷ AL Rae Centre for Genetics and Breeding, Massey University, Hamilton 3214, New Zealand.
⁸ College of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil.
⁹ DB Genética de Suínos, Patos de Minas 38706-000, MG, Brazil.

PMID: 35804531
PMCID: PMC9265114
DOI: 10.3390/ani12131632

Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

Simara Larissa Fanalli et al. Animals (Basel). 2022.

. 2022 Jun 25;12(13):1632.

doi: 10.3390/ani12131632.

Authors

Affiliations

¹ Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil.
² Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil.
³ College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia 74690-900, GO, Brazil.
⁴ GIGA Medical Genomics, Unit of Animal Genomics, University of Liège, 4000 Liège, Belgium.
⁵ Embrapa Pecuária Sudeste, São Carlos 70770-901, SP, Brazil.
⁶ College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA.
⁷ AL Rae Centre for Genetics and Breeding, Massey University, Hamilton 3214, New Zealand.
⁸ College of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil.
⁹ DB Genética de Suínos, Patos de Minas 38706-000, MG, Brazil.

PMID: 35804531
PMCID: PMC9265114
DOI: 10.3390/ani12131632

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.

Keywords: Longissimus lomborum; RNAseq; animal model; fatty acid; hepatic tissue; immune response; metabolism; transcriptome.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
Top 10 enriched process networks identified by MetaCore software from the list of differentially expressed genes (FDR 10%) in the liver of pigs fed with two different levels of soybean oil in the diet (1.5% and 3.0% of soybean oil).

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Key co-expressed genes correlated with blood serum parameters of pigs fed with different fatty acid profile diets.
Fanalli SL, Gomes JD, de Novais FJ, Gervásio IC, Fukumasu H, Moreira GCM, Coutinho LL, Koltes J, Amaral AJ, Cesar ASM. Fanalli SL, et al. Front Genet. 2024 Jul 3;15:1394971. doi: 10.3389/fgene.2024.1394971. eCollection 2024. Front Genet. 2024. PMID: 39021677 Free PMC article.
Pig models reveal the interplay between fatty acids and cytokines in skeletal muscle.
Ciconello FN, Tuggle CK, Gomes JD, da Silva BPM, de Castro Durval M, de Oliveira CS, Nascimento LE, Freitas LS, Koltes JE, Cesar ASM. Ciconello FN, et al. Sci Rep. 2025 Jun 4;15(1):19528. doi: 10.1038/s41598-025-04273-0. Sci Rep. 2025. PMID: 40467700 Free PMC article.
RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids.
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 JCC, Mourão GB, Coutinho LL, Fukumasu H, de Alencar SM, Luchiari Filho A, Cesar ASM. Fanalli SL, et al. Front Genet. 2023 Jan 25;14:1053021. doi: 10.3389/fgene.2023.1053021. eCollection 2023. Front Genet. 2023. PMID: 36816031 Free PMC article.
Brain fatty acid and transcriptome profiles of pig fed diets with different levels of soybean oil.
da Silva BP, 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 LCA, Mourão GB, Luchiari Filho A, Cesar ASM. da Silva BP, et al. BMC Genomics. 2023 Feb 28;24(1):91. doi: 10.1186/s12864-023-09188-6. BMC Genomics. 2023. PMID: 36855067 Free PMC article.

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Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

Affiliations

Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

Authors

Affiliations

Abstract

Conflict of interest statement

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