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.

Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality

“…Meanwhile, the expression pro les of lncRNAs in skeletal muscle tissues were also investigated and lncRNAs were found to be differentially expressed in samples with different genetic backgrounds. However, these studies in livestock have mainly been focused on sheep [10][11][12], cattle [13][14][15], chicken [16][17][18], and pigs [19][20][21].…”

Transcriptome-Wide Study of mRNAs and lncRNAs Modified by m6A RNA Methylation in the Longissimus Dorsi Muscle Development of Cattle-Yak

“…In previous studies, the production performance of cattle-yaks was significantly higher than that of yaks at two developmental stages, hence we selected the cattle-yaks aged six months and eighteen months to explore the transcriptome-wide m6A modifications profile [ 1 ]. First, we analyzed the marker genes associated with myoblast proliferation and regulation of skeletal muscle development in conjunction with the changes in production performance using qRT-PCR technology.…”

“…The String Tie software was used to reassemble transcripts of all samples [ 94 ], then the sample input data was considered as transcriptome data to conduct the lncRNA prediction and analysis combined with known lncRNA annotation information in NCBI and Ensembl databases. The screening and identification of lncRNAs underwent a series of strict steps, as in our previous report [ 1 ]. Finally, the detected peak position information was compared with the known lncRNAs annotation information in the NCBI and Ensembl databases.…”

“…In high-altitude hypoxic areas such as the Qinghai-Tibet Plateau, the production performance and meat quality of the yaks have been unable to meet human needs, while cattle-yaks have shown obvious hybrid vigor. In previous studies, the production performance of cattle-yaks at all growth stages was significantly higher than that of yaks [ 1 ]. At the same time, the meat quality of cattle-yaks has higher protein and lower fat content, which can satisfy the requirements of human health and high-quality diet better than yaks [ 2 , 3 ].…”

Characterization of N6-methyladenosine in cattle-yak testis tissue

“…Cattle-yaks exhibit excellent heterosis with respect to growth speed, disease resistance, drought tolerance, meat quality, and adaptability to the plateau environment ( 13 , 14 ). Meat from these cattle-yak hybrids, which are larger than yaks, contains higher levels of protein and lower fat content as compared to yak meat, thus fulfilling a need for the production of healthier high-quality foods fit for public consumption ( 15 ). However, this heterosis cannot be effectively leveraged owing to the fact that F1 male cattle-yaks exhibit an inability to produce sperm, resulting in sterility ( 16 ).…”