Genome-wide identification and analysis of long noncoding RNAs in longissimus muscle tissue from Kazakh cattle and Xinjiang brown cattle

Abstract

Objective: In recent years, lncRNAs have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the FPKM values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting FDR was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in KEGG pathways. We randomly selected eight lncRNA genes and validated them by RT-qPCR. Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the MAPK, Ras and PI3k/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.

Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle

“…In the process of detecting differentially expressed genes, the fold change (FC) represents the ratio of the expression levels between two samples (groups), and the false discovery rate (FDR) is measured by the p-value obtained by calibration. We finally chose fold change ≥ 1.5 and P value <0.05 as the screening criteria [3,6].…”

“…dorsi [2]. We previously studied differentially expressed circular RNAs between Kazakh cattle and Xinjiang brown cattle in the longissimus dorsi [3].…”

“…With the development of China's agricultural production, the cattle industry has been pursuing data-based changes in pursuit of quality. China has abundant resources in terms of local breeds, such as Qinchuan cattle (distributed in Shaanxi, and having strong bones and full muscles) [1], Kazakh cattle(distributed in Xinjiang, and exhibiting strong stress resistance and resistance to rough feeding) [2,3], Yanbian yellow cattle (distributed in Jilin, and having strong adaptability and tender meat) [4], and Xinjiang brown cattle (distributed in Xinjiang, and having large body and strong adaptability) [5,6]. These breeds of cattle have very unique growth, meat quality, disease resistance, milk quality and other excellent traits.…”

“…As one of the local yellow cattle breeds in China, Kazakh cattle are characterized by stable genetic quality, excellent production performance, good grazing performance, rough feeding resistance, strong adaptability and stress resistance and are deeply loved by farmers and herders [3,6]. Kazakh cattle are the leading species of the Xinjiang beef cattle industry [2,3,6]. Xinjiang Brown Cattle is an excellent new breed of grass-fed livestock that has independent intellectual property rights and is bred in China.…”

Biological functions of circRNAs and their progress in livestock and poultry

“…More recently, Yan et al. (2020) identified 5,177 circRNAs in longissimus dorsi samples from Kazakh cattle and Xinjiang brown cattle, of which 46 were differentially expressed. In addition, the prediction analysis showed two circRNAs (bta_circ_03789_1 and bta_circ_05453_1) function as miRNA sponges that may potentially regulate expression of the IGF1R to regulate muscle growth and development in cattle.…”