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. 2023 Nov;102(11):103035.
doi: 10.1016/j.psj.2023.103035. Epub 2023 Aug 18.

Identification of key genes related to intramuscular fat deposition in Beijing-You chicken by mRNA and miRNA transcriptome analysis

Kai Gai  1 , Yu Ge  1 , Dapeng Liu  2 , He Zhang  2 , Bailin Cong  1 , Shihao Guo  1 , Yizheng Liu  1 , Kai Xing  1 , Xiaolong Qi  1 , Xiangguo Wang  1 , Longfei Xiao  1 , Cheng Long  1 , Yong Guo  1 , Li Chen  3 , Xihui Sheng  4
Affiliations

Identification of key genes related to intramuscular fat deposition in Beijing-You chicken by mRNA and miRNA transcriptome analysis

Kai Gai et al. Poult Sci. 2023 Nov.

Abstract

Intramuscular fat (IMF) is an important factor affecting chicken quality. However, the age-related mechanism of IMF deposition has not yet been elucidated. In this study, the IMF, phospholipids (PL), triglycerides (TG), and fatty acid (FA) content in the breast muscle of Beijing-You chicken (BJY) at 1, 56, 98, and 120 d of age was measured, and mRNA and miRNA sequencing was integrated to explore the regulatory genes of IMF deposition. The results showed that the IMF content of BJY at 1 d of age was significantly higher than that at later stage of birth (P < 0.05). The transcriptome sequencing results showed that 7, 225 differentially expressed genes (DEGs) and 243 differentially expressed miRNAs (DE-miRNAs) were identified. The cluster analysis showed that the expression of DEGs and DE-miRNAs at 1 d of age was significantly different from that at later stages of birth. Furthermore, a potential mRNA-miRNA regulatory network related to IMF deposition was established by weighted gene co-expression network analysis (WGCNA); gga-miR-29c-3p-PIK3R1, gga-miR-6701-3p-PTEN, gga-miR-363-3p-PTEN, gga-miR-1563-WWP1, gga-miR-449c/d-5p-TRAF6, and gga-miR-6701-3p-BMPR1B were identified as key mRNA-miRNA pairs for the regulation of IMF deposition. These results will help elucidate the mechanism of IMF formation mediated by miRNAs in chickens, and provide a theoretical foundation for the genetic improvement of broiler meat quality.

Keywords: Beijing-You chicken; intramuscular fat; miRNA; transcriptome.

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Figures

Figure 1
Figure 1
The differential expression analysis of mRNAs. (A) Volcano plot of differentially expressed genes (DEGs) between different stages; significantly downregulated genes are represented as blue dots and significantly upregulated genes are represented as red dots. (B) Heatmap of DEGs by cluster analysis. n = 10.
Figure 2
Figure 2
Functional analysis of differentially expressed genes (DEGs) at d 1 vs. 56, 56 vs. 98 and 98 vs. 120 by Gene Set Enrichment Analysis (GSEA). The ordinate represented the enrichment score value, and the abscissa represented a ranked DEGs list correlation profile. n = 10.
Figure 3
Figure 3
Weighted gene co-expression network analysis of differentially expressed genes and traits in breast muscle of Beijing-You chicken (BJY). (A) Nine modules obtained by weighted gene co-expression network analysis (WGCNA). The dendrogram showed the co-expression clusters, the different colors indicated the co-expression modules. (B) Heat map showed module-trait relationships. Each row represented a module. Each column represented a trait. The red color indicated that there was a significantly positive correlation between this module and the trait, and the green color indicated a significantly negative correlation (P < 0.05). n = 10.
Figure 4
Figure 4
Volcano plot of differentially expressed mi-RNAs (DE-miRNAs) between different stages; significantly downregulated genes are represented as blue dots and significantly upregulated genes are represented as red dots. n = 10.
Figure 5
Figure 5
Functional analysis of miRNA target genes. (A) The top 200 significant Gene Ontology (GO) enrichment terms. (B) The top 20 significant terms by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. n = 10.
Figure 6
Figure 6
Analysis of the interaction between mRNA and miRNA. (A) Protein-protein interaction (PPI) network of significant genes in weighted gene co-expression network analysis (WGCNA). (B) mRNA-miRNA regulatory network. (C) A core network identified by the Degree algorithm in Cytoscape. The cyan circle represented the differentially expressed genes (DEGs) in the cyan module, the blue circle represented the DEGs in the blue module, and the pink box represented the DE-miRNAs. n = 10.
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References

    1. Assmann T.S., Riezu-Boj J.I., Milagro F.I., Martínez J.A. Circulating adiposity-related microRNAs as predictors of the response to a low-fat diet in subjects with obesity. J. Cell Mol. Med. 2020;24:2956–2967. - PMC - PubMed
    1. Bosco A.D., Mattioli S., Ruggeri S., Mugnai C., Castellini C. Effect of slaughtering age in different commercial chicken genotypes reared according to the organic system: 2. Fatty acid and oxidative status of meat. Italian J. Anim. Sci. 2014;13:462–466.
    1. Cameron N.D., Enser M.B. Fatty acid composition of lipid in Longissimus dorsi muscle of Duroc and British Landrace pigs and its relationship with eating quality. Meat. Sci. 1991;29:295–307. - PubMed
    1. Cantley L.C. The phosphoinositide 3-kinase pathway. Science. 2002;296:1655–1657. - PubMed
    1. Chang G.B., Lei L.L., Zhang X.Y., Wang K.H., Chen R., Luan D.Q., Chen G.H. Development rule of intramuscular fat content in chicken. J. Anim. Vet. Adv. 2010;9:297–298.