黔北黑猪不同骨骼肌内脂肪沉积相关 lncRNAs的鉴定

Identification of lncRNAs Related to Fat Deposition in Different Skeletal Muscle of Qianbei Black Pigs

摘要

旨在挖掘不同类型骨骼肌内脂肪沉积相关的候选长链非编码RNA（long nocoding RNA， lncRNA）。取亲缘关系相近的9头健康黔北黑猪母猪（日龄180±11 d，体重60±7 kg），随机分成3组，分别采集背最长肌和腰大肌，通过RNA-seq构建lncRNAs表达谱，筛选差异表达lncRNAs并经qRT-PCR进行验证，采用生物信息学方法预测差异表达的lncRNAs的靶基因，并对其进行GO和KEGG功能富集分析，从中找出肌内脂肪沉积相关的lncRNAs，同时构建lncRNA-mRNA调控网络。在黔北黑猪两种不同骨骼肌中注释到4 232个lncRNAs，从中鉴定出45个差异表达lncRNAs（23个下调表达，22个上调表达）；qRT-PCR结果提示这些lncRNA的表达模式与RNA-seq数据高度一致。GO和KEGG分析结果表明，差异表达lncRNAs的靶基因主要富集在磷脂、脂质和脂肪酸转运、脂肪酸分解及雌激素受体信号通路负调控等GO条目和ABC转运蛋白、内吞作用、胆汁分泌、代谢途径、过氧化物酶体等信号通路上；lncRNA-mRNA调控网络表明，TCONS_00123816和TCONS_00014197可能分别通过PPAR信号通路和Wnt信号通路调控肌内脂肪沉积。TCONS_00123816和TCONS_00014197可能通过其靶基因调控猪骨骼肌内脂肪沉积。这些研究发现将为深入解析不同类型骨骼肌脂肪沉积的机理提供数据支撑，对辅助选育优质肉用品种具有重要意义。

Abstract

This study aims to explore the candidate lncRNAs related to intramuscular fat deposition in different types of skeletal muscle of Qianbei black pigs. Nine healthy female Qianbei black sows (180±11 days old and 60±7 kg in weight) with close kinship are randomly divided into 3 groups. Samples are collected from the longissimus dorsi and psoas major muscles. RNA-seq is used to construct lncRNA expression profiles, and differentially expressed lncRNAs are screened and validated by qRT-PCR. Bioinformatics methods are employed to predict the target genes of these differentially expressed lncRNAs, followed by GO and KEGG functional enrichment analyses to identify lncRNAs related to intramuscular fat deposition. Additionally, an lncRNA-mRNA regulatory network is constructed. A total of 4 232 lncRNAs are annotated in the two skeletal muscles of Qianbei black pigs, from which 45 differentially expressed lncRNAs are identified (23 downregulated and 22 upregulated). The qRT-PCR results indicate that the expression patterns are highly consistent with the RNA-seq data. GO and KEGG analysis reveal that the target genes of differentially expressed lncRNAs are mainly enriched in GO terms such as phospholipid, lipid and fatty acid transport, fatty acid breakdown, and negative regulation of estrogen receptor signaling pathways, as well as signaling pathways involving ABC transporters, endocytosis, bile secretion, metabolic pathways, and peroxisomes. The lncRNA-mRNA network indicates that TCONS_00123816 and TCONS_00014197 may regulate intramuscular fat deposition through the PPAR signaling pathway and the Wnt signaling pathway, respectively. TCONS_00123816 and TCONS_00014197 may regulate skeletal muscle fat deposition through their target genes in pig. These findings provide data support for in-depth analysis of the mechanisms of fat deposition in different types of skeletal muscle and hold significant implications for assisting in the breeding of high-quality meat varieties.

关键词

黔北黑猪 / lncRNAs / 背最长肌 / 腰大肌 / 脂肪沉积

Key words

Qianbei black pig / lncRNAs / longissimus dorsi muscle / psoas major muscle / fat deposition

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基金资助

贵州省科学技术厅高层次创新型人才培养项目（千层次）(2022-(2020)-044)