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Article

Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle

1
Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234, s/n, Fazenda Canchim, São Carlos, SP 339, Brazil
2
Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP 13418-900, Brazil
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Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-905, Brazil
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Department of Animal Sciences, North Dakota State University, Fargo, ND 58105, USA
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Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, SP 13635-900, Brazil
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Department of Agri-Food Industry, Food and Nutrition, “Luiz de Queiroz” College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP 13418-900, Brazil
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Embrapa Informática Agropecuária, Campinas, SP 13083-886, Brazil
*
Author to whom correspondence should be addressed.
Genes 2021, 12(1), 67; https://doi.org/10.3390/genes12010067
Received: 2 December 2020 / Revised: 26 December 2020 / Accepted: 31 December 2020 / Published: 6 January 2021
(This article belongs to the Section Animal Genetics and Genomics)
MicroRNAs (miRNAs) are key regulators of gene expression, potentially affecting several biological processes, whose function can be altered by sequence variation. Hence, the integration of single nucleotide polymorphisms (SNP) and miRNAs can explain individual differences in economic traits. To provide new insights into the effects of SNPs on miRNAs and their related target genes, we carried out a multi-omic analysis to identify SNPs in miRNA mature sequences (miR-SNPs) associated with fatty acid (FA) composition in the Nelore cattle. As a result, we identified 3 miR-SNPs in different miRNAs (bta-miR-2419-3p, bta-miR-193a-2, and bta-miR-1291) significantly associated with FA traits (p-value < 0.02, Bonferroni corrected). Among these, the rs110817643C>T, located in the seed sequence of the bta-miR-1291, was associated with different ω6 FAs, polyunsaturated FA, and polyunsaturated:saturated FA ratios. Concerning the other two miR-SNPs, the rs43400521T>C (located in the bta-miR-2419-3p) was associated with C12:0 and C18:1 cis-11 FA, whereas the rs516857374A>G (located in the bta-miR-193a-2) was associated with C18:3 ω6 and ratio of ω6/ω3 traits. Additionally, to identify potential biomarkers for FA composition, we described target genes affected by these miR-SNPs at the mRNA or protein level. Our multi-omics analysis outlines the effects of genetic polymorphism on miRNA, and it highlights miR-SNPs and target candidate genes that control beef fatty acid composition. View Full-Text
Keywords: polymorphism; association analysis; miRNAs; Bos indicus; beef quality polymorphism; association analysis; miRNAs; Bos indicus; beef quality
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MDPI and ACS Style

Cardoso, T.F.; Coutinho, L.L.; Bruscadin, J.J.; da Silva Diniz, W.J.; Petrini, J.; Andrade, B.G.N.; de Oliveira, P.S.N.; Poleti, M.D.; Cesar, A.S.M.; da Silveira, J.C.; Chiaratti, M.R.; Zerlotini, A.; Mourão, G.B.; de Almeida Regitano, L.C. Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle. Genes 2021, 12, 67. https://doi.org/10.3390/genes12010067

AMA Style

Cardoso TF, Coutinho LL, Bruscadin JJ, da Silva Diniz WJ, Petrini J, Andrade BGN, de Oliveira PSN, Poleti MD, Cesar ASM, da Silveira JC, Chiaratti MR, Zerlotini A, Mourão GB, de Almeida Regitano LC. Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle. Genes. 2021; 12(1):67. https://doi.org/10.3390/genes12010067

Chicago/Turabian Style

Cardoso, Tainã Figueiredo, Luiz Lehmann Coutinho, Jennifer Jessica Bruscadin, Wellison Jarles da Silva Diniz, Juliana Petrini, Bruno Gabriel Nascimento Andrade, Priscila Silva Neubern de Oliveira, Mirele Daiana Poleti, Aline Silva Mello Cesar, Juliano Coelho da Silveira, Marcos Roberto Chiaratti, Adhemar Zerlotini, Gerson Barreto Mourão, and Luciana Correia de Almeida Regitano. 2021. "Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle" Genes 12, no. 1: 67. https://doi.org/10.3390/genes12010067

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