Abstract
Simple SummaryThis study provides a clear and accurate dynamic profile of circRNAs in skeletal muscle and subcutaneous fat of Ningxiang pig. The results include high-quality genomic data, and help to elucidate the roles of circRNAs in regulation of protein and lipid synthesis and metabolism providing new ideas for further understanding of the molecular mechanisms governing pork quality traits. Recently, thousands of circular RNAs have been reported in different pig breeds. However, researches on the temporal and spatial expression patterns of circRNA over the period of animal growth are limited. Here, we systematically analyzed circRNAs in skeletal muscle and subcutaneous fat in four growth time points (30 days, 90 days, 150 days and 210 days after birth) of a Chinese native pig breed, Ningxiang pigs. A total of 1171 differentially expressed (DE) circRNAs between muscle and fat were identified, including 562 upregulated and 609 downregulated circRNAs. KEGG pathway enrichment analysis of these DE circRNAs revealed that host genes were mainly involved in glycogen metabolism signaling pathways, muscle development signaling pathways such as ErbB pathway and adipocytokine signaling pathways and AMPK signaling pathways and fatty acid biosynthesis. The circRNAs have striking spatiotemporal specificity in the form of dynamic expression at 90 d. Short Time-Series Expression Miner analysis showed multiple model spectra that are significantly enriched with time changes in muscle and fat. Our findings provide new ideas and perspectives about the role of circular RNAs and their targeting relations with mRNA and miRNA in skeletal muscle and fat tissue during pig growth.
Highlights
After years of animal breeding programs, the lean meat percentage of commercial pigs has been considerably improved, but current living standards have prompted consumers to seek pork with high meat quality
It has been reported that the synthesis of unsaturated lipids is regulated by multiple genes, such as peroxisome proliferator activated receptor alpha (PPARα), fatty acid binding protein 4 (FABP 4), lipoprotein lipase (LPL) [8], CCAAT enhancer binding protein alpha (C/EBPα) [9], patatin-like phospholipase domain containing 3 (PNPLA3) [10], malic enzyme 1 (ME1) [11] and 2,4-dienoyl-CoA reductase 1 (DECR1) [12]
To perform comprehensive profiling of circular RNA in pig, we performed total RNA sequencing in two major tissues of lipid anabolic metabolism and across four developmental stages (30 d, 90 d, 150 d and 210 d after birth)
Summary
After years of animal breeding programs, the lean meat percentage of commercial pigs has been considerably improved, but current living standards have prompted consumers to seek pork with high meat quality. Polyunsaturated fatty acids (PUFAs) are indispensable essential fatty acids for the body, while long-chain (≥C20) polyunsaturated fatty acids (LC-PUFAs) are highly biologically active forms of PUFAs, and their biological functions have become a significant research topic in international pig research communities [6,7]. This characteristic is a valuable trait of Ningxiang pig. As a research model, Ningxiang pig is of considerable significance for studies exploring genes related to meat quality traits and their expression patterns
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