Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

Abstract

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

Keywords: Bos grunniens; cattle-yak; ceRNA; circRNA; lncRNA; skeletal muscle; transcriptome.

FIGURE 1

The description of identified lncRNAs and circRNAs. (A) Screening of the candidate lncRNAs in longissimus dorsi muscle. (B) The length distribution of the novel lncRNAs. (C) Exon number distribution of novel lncRNAs. (D) The classification of novel lncRNAs. (E) The structure type pie chart of circRNAs. (F) The length distribution of circRNAs.

FIGURE 2

Comparative analysis of the differentially expressed mRNAs and ncRNAs between cattle-yaks and yaks. The specific and shared mRNAs (A), lncRNAs (B), and circRNAs (C) between the two groups. The analysis of differentially expressed mRNAs (D), lncRNAs (E), and circRNAs (F) between two groups. Note: The red and green points represented upregulated and downregulated mRNAs, lncRNAs, and circRNAs, respectively. The gray points represented no significant differences. The gray vertical lines showed |log2FC| = 1, and the gray horizontal lines showed p = 0.05.

FIGURE 3

(A) GO analysis with the top 10 enrichment biological processes for DEMs, DELs targets, and DECs host genes between cattle-yaks and yaks. KEGG analysis with the top 20 KEGG enrichment pathways for DEMs (B), DELs target genes (C), and DECs host genes (D) between the cattle-yaks and yaks.

FIGURE 4

Functional analysis of 117 differentially expressed genes associated with muscle development and fatness between the cattle-yak and yak. GO (A) and KEGG (B) analysis.

FIGURE 5

The ceRNA co-regulation network. The blue circle, yellow box, red triangle and green V-type represented the differentially expressed mRNAs, lncRNAs, circRNAs, and miRNA, respectively. The solid line indicated the co-regulation between miRNAs and other transcripts. The dotted line indicated the co-regulation between the lncRNAs and mRNAs.

FIGURE 6

The results of the real-time quantitative PCR validation of the expression level. ** indicates p < 0.01, * indicates p < 0.05. The data represented the mean ± SEM from three biological replicates, and each measurement was repeated 3 times.