Identification of Candidate Circular RNAs Underlying Intramuscular Fat Content in the Donkey.

Bojiang Li,Chunyu Feng,Zhe Wang,David M Irwin,Shiyu Zhu,Junpeng Zhang,Xiaoying Zhang,Shuyi Zhang

doi:10.3389/fgene.2020.587559

Abstract

Intramuscular fat (IMF) content is a crucial indicator of meat quality. Circular RNAs (circRNAs) are a large class of endogenous RNAs that are involved in many physiological processes. However, the expression and function of circRNA in IMF in the donkey remains unresolved. Here we performed an expression profiling of circRNAs in the donkey longissimus dorsi muscle and identified 12,727 candidate circRNAs. Among these, 70% were derived from the exons of protein genes. Furthermore, a total of 127 differentially expressed (DE) circRNAs were identified in high (H) and low (L) IMF content groups, including 63 upregulated and 64 downregulated circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the host genes of the DE circRNAs showed that the host genes were enriched in lipid metabolism related GO terms (e.g., fatty acid beta-oxidation using acyl-CoA dehydrogenase and MLL3/4 complex), and signaling pathways (e.g., TGF-beta and lysine degradation signaling pathway). Further analyses indicated that 127 DE circRNAs were predicted to potentially interact with miRNAs, leading to the construction of circRNA-miRNA regulatory network. Multiple circRNAs can potentially function as sponges of miRNAs that regulate the differentiation of adipocytes. Our results provide valuable expression profile information for circRNA in the donkey and new insight into the regulatory mechanisms of circRNAs in the regulation of IMF content.

Highlights

The donkey (Equus asinus) is an important livestock animal in many countries including China and Italy (Polidori et al, 2015; Zhang X. et al, 2019), and plays a crucial role in human agricultural society by providing various products, acting as a draft force and transportation (Xia et al, 2019)
Our results indicate that the density distribution of circRNA expression was not significantly different between the H and L Intramuscular fat (IMF) content groups (Figure 2A), 127 differentially expressed (DE) circRNAs were identified, including upregulated and downregulated circRNAs in the H IMF content group (Figures 2B,C)
Our current study revealed that many DE circRNAs may act as endogenous sponges of miRNAs including miR-429 (Peng et al, 2016), miR-224 (Zhang Y. et al, 2019), miR-125a-5p (Du et al, 2018), miR-223 (Li F. et al, 2019), miR-145 (Guo et al, 2012), miR-302a (Jeong et al, 2014), miR181a (Zhang Z. et al, 2019), miR-144 (Shen et al, 2018), miR-199a-5p (Shi et al, 2014), and miR-127 (Gao et al, 2019) that are involved in the regulation of adipogenesis. miR125a-5p is negatively involved with IMF content by targeting KLF13 and ELOVL6 (Du et al, 2018)

Summary

Introduction

The donkey (Equus asinus) is an important livestock animal in many countries including China and Italy (Polidori et al, 2015; Zhang X. et al, 2019), and plays a crucial role in human agricultural society by providing various products (meat, milk, and leather), acting as a draft force and transportation (Xia et al, 2019). With the increasing mechanization of the world, donkey meat production from young males has improved the quality of the meat and attracted more customers for its consumption (Lorenzo et al, 2014). Donkey has increasingly become an important meat producing livestock. The protein content of donkey meat is 22.8%, and the potassium and phosphorus content are 343 and 212 mg per100 g, respectively (Polidori et al, 2008)

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Discussion

Conclusion