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

Abstract

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.

Keywords: Bos indicus; association analysis; beef quality; miRNAs; polymorphism.

Figure 1

Overview of the multi-omics analysis approach for identification of polymorphisms in miRNA mature sequence associated to fatty acid composition in the Nelore cattle.

Figure 2

In silico analysis of potential impact of miR-SNPs. Secondary structure predicting the impact of the miR-SNPs in pre-miRNAs sequences: (A) Secondary structure of bta-mir-2419 with the rs43400521:T>C miR-SNP, (B) Secondary structure of bta-mir-193a-2 with the rs516857374:A>G miR-SNP and (C) Secondary structure of bta-mir-1291 with the rs110817643:C>T miR-SNP. The secondary structures of the pre-miRNAs were predicted by inputting two transcript sequences, corresponding to both alleles of the miR-SNPs, i.e., either the major (top) or minor (bottom) allele submitted to RNAfold. Figures and minimum free energy (MFE) values were generated by RNAfold.

Figure 3

Association analysis of rs43400521T>C miR-SNP genotype in the bta-miR-2419-3p. (A) Least square means for the fatty acids associated traits identified by Gemma software (CC, n = 326; TC, n = 46; and TT, n = 2). (B) Least squares means for the genes associated identified by Gemma software (CC, n = 164 and TC, n = 28).

Figure 4

Association analysis of rs516857374A>G genotype in the bta-miR-193a-2. Least square means for the fatty acids associated traits identified by Gemma software (AA, n = 130; GA, n = 182; and GG, n = 62).

Figure 5

String network showing the genes whose expression decreases in response to G allele of the rs516857374A>G located in the bta-miR-193a-2 mature sequence. The network nodes are proteins and the edges represent the predicted functional associations. Each colored line represents different evidence for each interaction (red: fusion; green: neighborhood; blue: co-occurrence; purple: experimental; yellow: text mining; light blue: database; black: co-expression).

Figure 6

Association analysis of rs110817643C>T genotype in the bta-miR-1291. Least square means for the fatty acids associated traits identified by Gemma software (CC, n = 345; and TC, n = 29).

Figure 7

(A) RNAhybrid analysis of C allele of the rs110817643C>T located in the seed sequence of the bta-miR-1291 (red sequence) and corresponding target sequences on TCEA2 and BCAR1 3’UTR (green sequence). The red triangle marks the SNP positions. These interactions were predicted to be lost, in both target genes, for the miRNA sequence corresponding to the T allele of the rs110817643C>T (TCEA2-rs110817643:T-MFE = −30.8, p-value = 0.08; BCAR1-rs110817643:T-MFE = −28.5, p-value = 0.07). (B) Least squares means by genotype for rs110817643C>T miR-SNP located in the bta-miR-1291. Least square means for the proteins associated identified by Gemma software (CC, n = 90; and TC, n = 15).