Abstract
Simple SummaryThis study shows the transcription profiles and the functional network in lncRNA and mRNA in the subcutaneous adipose tissue of Ningxiang piglets in four stages of development (piglets, nursery pigs, early fattening, and late fattening). A total of 2872 novel lncRNAs have now been determined. A total of 10,084 DEmRNAs and 931 DElncRNAs were determined. Interestingly, most DEmRNAs were up-regulated in the piglet stage and, in contrast, DElncRNAs were up-regulated in the late fattening stage. A complicated interaction between mRNAs and lncRNAs was determined via STEM and WGCNA, demonstrating that lncRNAs are an essential regulatory component in mRNAs. Modules 2 and 5 shows a similar mode of transcriptions for both mRNA and lncRNA, which are mainly involved in steroid biosynthesis, glycosphingolipid biosynthesis, metabolic pathways, and glycerolipid metabolism. The transcription levels of mRNAs and lncRNAs for both modules were higher in the early and late fattening stage. This may be explained by the active fatty acids, sterols, steroids, and lipid-related metabolic activity in the subcutaneous adipose tissue during the early and late fattening stage.Ningxiang pigs, a Chinese bred pig known for its tender meat and high quality unsaturated fatty acids. This study discovers the transcription profiles and functional networks in long non-coding RNA (lncRNA) and messenger RNA (mRNA) in subcutaneous adipose tissue. Subcutaneous adipose tissue was collected from piglet, nursery pig, early fattening, and late fattening stage of Ningxiang piglets, and lncRNA and mRNA transcription of each stage was profiled. A total of 339,204,926 (piglet), 315,609,246 (nursery), 266,798,202 (early fattening), and 343,740,308 (late fattening) clean reads were generated, and 2872 novel lncRNAs were identified. Additionally, 10,084 differential mRNAs (DEmRNAs) and 931 differential lncRNAs were determined. Most DEmRNAs were up-regulated in the piglet stage, while they were down-regulated in late fattening stage. A complicated interaction between mRNAs and lncRNAs was identified via STEM and WGCNA, demonstrated that lncRNAs are a significant regulatory component in mRNAs. The findings showed that modules 2 and 5 have a similar mode of transcription for both mRNA and lncRNA, and were mainly participated in steroid biosynthesis, glycosphingolipid biosynthesis, metabolic pathways, and glycerolipid metabolism. The mRNAs and lncRNAs transcription levels of both modules was higher in the early and late fattening stage, which may be due to the active activity of the metabolism in relation to fatty acids, sterols, steroids, and lipids in the subcutaneous adipose tissue during the early and late fattening stage. These findings could be expected to result in further research of the functional properties of lncRNA from subcutaneous adipose tissue at different stages of development in Ningxiang pigs.
Highlights
There are more than 100 breeds of pigs in China, and one-third of the world’s pig breeds are found in China [1]
Among the common differential messenger RNA (mRNA), we found that FADS2, CYP3A29, CYP2C42, AGMO, PLCB4, leptin receptor (LEPR), CES1D participated in lipid metabolism, while IGF2, IGFALS, and FGFR4 were involved in cell differentiation and proliferation
Among the DElncRNAs, we found that CYP3A29, IGFALS, Carboxylesterase 1 (CES1), LEPR, and placenta-specific 8 (PLAC8) served as target genes for MSTRG.35604.2, MSTRG.26481.9, MSTRG.23976.1, MSTRG.40648.1, and MSTRG.27163.1
Summary
There are more than 100 breeds of pigs in China, and one-third of the world’s pig breeds are found in China [1]. Ningxiang pigs have a breeding history of more than a thousand years in China. They are renowned for their tender and juicy meat, their unique taste, and the high quality of unsaturated fatty acids. Because of their breeding history and advantages, Ningxiang pigs have become a significant livestock resource and a geographical representation of the Chinese agricultural product [3]. Compared to other pig species, Ningxiang pigs have more than 5% of intramuscular adipose tissues [5,6]. High intramuscular fat content improves the meat quality and taste in Ningxiang pigs. Ningxiang pigs showed better disease resistance [7] and pronounced genetic characteristic such as strong adaptability and high reproductive capacity [2]
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