Table_9_Transcriptome Analysis Suggests the Roles of Long Intergenic Non-coding RNAs in the Growth Performance of Weaned Piglets.XLSX

Long intergenic non-coding RNAs (lincRNAs) have been considered to play a key regulatory role in various biological processes. An increasing number of studies have utilized transcriptome analysis to obtain lincRNAs with functions related to cancer, but lincRNAs affecting growth rates in weaned piglets are rarely described. Although lincRNAs have been systematically identified in various mouse tissues and cell lines, studies of lincRNA in pigs remain rare. Therefore, identifying and characterizing novel lincRNAs affecting the growth performance of weaned piglets is of great importance. Here, we reconstructed 101,988 lincRNA transcripts and identified 1,078 lincRNAs in two groups of longissimus dorsi muscle (LDM) and subcutaneous fat (SF) based on published RNA-seq datasets. These lincRNAs exhibit typical characteristics, such as shorter lengths and lower expression relative to protein-encoding genes. Gene ontology analysis revealed that some lincRNAs could be involved in weaned piglet related processes, such as insulin resistance and the AMPK signaling pathway. We also compared the positional relationship between differentially expressed lincRNAs (DELs) and quantitative trait loci (QTL) and found that some of DELs may play an important role in piglet growth and development. Our work details part of the lincRNAs that may affect the growth performance of weaned piglets and promotes future studies of lincRNAs for molecular-assisted development in weaned piglets.

基因间长链非编码RNA（long intergenic non-coding RNAs，lincRNAs）被认为在多种生物学过程中发挥关键调控作用。已有越来越多的研究通过转录组分析筛选得到与癌症功能相关的lincRNAs，但针对影响断奶仔猪生长速率的lincRNAs的报道仍较为匮乏。尽管已在多种小鼠组织和细胞系中完成了lincRNAs的系统鉴定，但猪源lincRNAs的相关研究仍寥寥无几。因此，鉴定并表征影响断奶仔猪生长性能的新型lincRNAs具有重要的科研价值。本研究基于已发表的RNA测序（RNA-seq）数据集，在背最长肌（longissimus dorsi muscle，LDM）与皮下脂肪（subcutaneous fat，SF）的两组样本中重构得到101,988条lincRNA转录本，并鉴定出1,078个lincRNAs。此类lincRNAs具备典型特征：相较于蛋白编码基因，其转录本长度更短、表达水平更低。基因本体论（Gene Ontology）分析结果显示，部分lincRNAs可能参与断奶仔猪相关生物学过程，例如胰岛素抵抗与AMPK信号通路。本研究还对差异表达lincRNAs（differentially expressed lincRNAs，DELs）与数量性状基因座（quantitative trait loci，QTL）的位置关联进行了分析比对，发现部分DELs可能在仔猪生长发育过程中发挥关键调控作用。本研究详细阐明了部分可能影响断奶仔猪生长性能的lincRNAs，可为未来开展针对断奶仔猪分子辅助选育的lincRNAs研究提供重要参考。