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. 2024 Feb 23;14(5):695.
doi: 10.3390/ani14050695.

Genome-Wide Transcriptome Profiling Reveals the Mechanisms Underlying Hepatic Metabolism under Different Raising Systems in Yak

Mengfan Zhang  1   2 , Xita Zha  3 , Xiaoming Ma  1   2 , Yongfu La  1   2 , Xian Guo  1   2 , Min Chu  1   2 , Pengjia Bao  1   2 , Ping Yan  1   2 , Xiaoyun Wu  1   2 , Chunnian Liang  1   2
Affiliations

Genome-Wide Transcriptome Profiling Reveals the Mechanisms Underlying Hepatic Metabolism under Different Raising Systems in Yak

Mengfan Zhang et al. Animals (Basel). .

Abstract

Yak meat is nutritionally superior to beef cattle but has a low fat content and is slow-growing. The liver plays a crucial role in lipid metabolism, and in order to determine whether different feeding modes affect lipid metabolism in yaks and how it is regulated, we employed RNA sequencing (RNA-seq) technology to analyze the genome-wide differential gene expression in the liver of yaks maintained under different raising systems. A total of 1663 differentially expressed genes (DEGs) were identified (|log2FC| ≥ 0 and p-value ≤ 0.05), including 698 down-regulated and 965 up-regulated genes. According to gene ontology (GO) and KEGG enrichment analyses, these DEGs were significantly enriched in 13 GO terms and 26 pathways (p < 0.05). Some DEGs were enriched in fatty acid degradation, PPAR, PI3K-Akt, and ECM receptor pathways, which are associated with lipid metabolism. A total of 16 genes are well known to be related to lipid metabolism (e.g., APOA1, FABP1, EHHADH, FADS2, SLC27A5, ACADM, CPT1B, ACOX2, HMGCS2, PLIN5, ACAA1, IGF1, FGFR4, ALDH9A1, ECHS1, LAMA2). A total of 11 of the above genes were significantly enriched in the PPAR signaling pathway. The reliability of the transcriptomic data was verified using qRT-PCR. Our findings provide new insights into the mechanisms regulating yak meat quality. It shows that fattening improves the expression of genes that regulate lipid deposition in yaks and enhances meat quality. This finding will contribute to a better understanding of the various factors that determine yak meat quality and help develop strategies to improve yield and quality.

Keywords: RNA-seq; fattening; lipid metabolism; liver; yak meat.

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Conflict of interest statement

The authors declare no conflicts of interest. The author who is not in the same organization as the other authors, and the organization he belongs to do not have a conflict of interest with this experiment.

Figures

Figure 1
Figure 1
Statistics of differentially expressed genes in the grazing group and the fattening group: (a) Volcano map of the number of differentially expressed genes. (b) Cluster analysis of the number of differentially expressed genes.
Figure 2
Figure 2
GO item enrichment analysis: (a) Scatterplot diagram of differentially expressed gene GO enrichment analysis; (b) scatterplot of GO enrichment analysis of up-regulated differentially expressed genes; (c) scatterplot of GO enrichment analysis of down-regulated differentially expressed genes.
Figure 3
Figure 3
Scatterplot diagram of KEGG enrichment analysis of differentially expressed genes.
Figure 4
Figure 4
Sankey map of differentially expressed genes: (a) Sankey map of the KEGG enrichment analysis of up-regulated differentially expressed genes; (b) Sankey map of the KEGG enrichment analysis of down-regulated differentially expressed genes.
Figure 5
Figure 5
Significant enrichment pathway of differentially expressed genes: (a) PI3K-Akt signaling pathway; (b) ECM-receptor signaling pathway; (c) PPAR signaling pathway; (d) fatty acid degradation pathway.
Figure 6
Figure 6
Validation of RNA-Seq results via RT-qPCR.
See this image and copyright information in PMC

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