Abstract

Background

   Intramuscular fat (IMF) content has become one of the most important
   indicators for measuring meat quality, and levels of IMF are affected
   by various genes. Long non-coding RNAs (lncRNAs) are widely expressed
   non-coding RNAs that play an important regulatory role in a variety of
   biological processes; however, research on the lncRNAs involved in
   sheep IMF deposition is still in its infancy. Aohan fine-wool sheep
   (AFWS), one of China’s most important meat-hair, dual-purpose sheep
   breed, provides a great model for studying the role of lncRNAs in the
   regulation of IMF deposition. We identified lncRNAs by RNA sequencing
   in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages:
   2 months (Mth-2) and 12 months (Mth-12).

Results

   We identified a total of 26,247 genes and 6935 novel lncRNAs in LTL
   samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were
   differentially expressed. We then compared the structural
   characteristics of lncRNAs and mRNAs. We obtained target genes of
   differentially expressed lncRNAs (DELs) and performed enrichment
   analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes
   and Genomes (KEGG). We found that target mRNAs were enriched in
   metabolic processes and developmental pathways. One pathway was
   significantly enriched, namely tight junction. Based on the analysis of
   critical target genes, we obtained seven candidate lncRNAs that
   potentially regulated lipid deposition and constructed a lncRNA-mRNA
   co-expression network that included MSTRG.4051.3-FZD4,
   MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1,
   MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We
   speculated that these candidate lncRNAs might play a role by regulating
   the expression of target genes. We randomly selected five mRNAs and
   five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.

Conclusions

   Our study identified the differentially expressed mRNAs and lncRNAs
   during intramuscular lipid deposition in Aohan fine-wool sheep. The
   work may widen the knowledge about the annotation of the sheep genome
   and provide a working basis for investigating intramuscular fat
   deposition in sheep.

Supplementary Information

   The online version contains supplementary material available at
   10.1186/s12864-021-07385-9.

   Keywords: Intramuscular fat, Aohan fine-wool sheep, Lipid deposition,
   Long non-coding RNAs, Co-expression analysis

Background

   High-quality lamb meat is becoming increasingly popular as living
   standards improve and dietary patterns change. Currently, evaluations
   of the meat quality of livestock have revealed that the content of
   intramuscular fat (IMF) is lower in carcass fats, yet IMF has a
   critically important influence on the edibility and flavor of muscle
   meat [[39]1]. Indeed, the quantity of IMF has become one of the most
   critical parameters of meat quality indicators, as it is considered to
   be positively related to meat quality and texture [[40]2, [41]3]. When
   a certain amount of fat is deposited between the muscle bundles and
   muscle fibers, the marbled section of the meat has a high score, and
   the meat is fresh and juicy, which is often considered ideal [[42]4,
   [43]5]. The selective deposition of fat can improve production
   efficiency and play a key role in improving meat quality. This practice
   is also a major focus and challenge of modern livestock breeding
   [[44]6]. Therefore, ensuring the appropriate deposition of IMF in lean
   meat can enhance the future quality of sheep meat.

   Studies have shown that intramuscular lipid deposition is affected by
   multiple genes and signaling pathways, such as the FAS, FAM134B, and
   HSL genes and the Wnt and AMPK signaling pathways [[45]7–[46]9].
   Recently, long non-coding RNAs (lncRNAs) have received increased
   attention for their wide-ranging functions. LncRNAs refer to a class of
   non-coding RNAs longer than 200 nt in length [[47]10]. Most lncRNAs
   have significant temporal and spatial expression specificity [[48]11,
   [49]12] and have low sequence conservation among species
   [[50]13–[51]15]. LncRNAs can be divided into five types based on their
   positions relative to neighboring protein-coding genes: intronic
   lncRNAs, bidirectional lncRNAs, sense lncRNAs, intergenic lncRNAs and
   antisense lncRNAs [[52]16].

   LncRNAs can regulate various life activities of the body, including
   epigenetic regulation, transcriptional regulation and
   post-transcriptional regulation [[53]17–[54]19]. The most common
   regulation methods of lncRNAs include cis-regulation of the
   transcription of neighboring protein-coding genes and the
   trans-regulation of non-adjacent genes. In addition, lncRNAs can
   interact with miRNAs to affect the post-transcriptional translation of
   related mRNAs [[55]20–[56]22]. Studies have shown that lncRNAs can play
   direct or indirect roles in the process of lipid accumulation [[57]23].
   SRA (steroid receptor RNA activator) is one of the earliest discovered
   lncRNAs and plays an important role in lipid metabolism. SRA can bind
   to peroxisome proliferator-activated receptor gamma (PPAR γ) and
   enhance PPAR γ activity, thereby promoting the differentiation of
   pre-adipocytes [[58]24]. A study of the expression levels of lncRNAs in
   the IMF of Jinhua and Landrace pigs revealed a total of 119
   differentially expressed lncRNAs (DELs), six of which were involved in
   fat deposition and lipid metabolism-related pathways [[59]25].
   Furthermore, an analysis of transcriptome data from IMF in Inner
   Mongolia goats revealed that 1472 lncRNAs were involved in adipocyte
   growth regulation and morphological changes of adipocytes [[60]26].
   Another study has shown that lncRNAs can play a key regulatory role in
   fat deposition in sheep tails [[61]27]. Overall, these findings
   demonstrate that lncRNAs can regulate lipid deposition through a
   variety of regulatory mechanisms. However, few studies have assessed
   the roles of lncRNAs in intramuscular lipid deposition in sheep.

   Aohan fine-wool sheep (AFWS) is an important meat-hair, dual-purpose
   sheep breed in China that grows rapidly early in development. The
   elimination of male lambs for fat lamb production can increase both
   hair and meat gains as well as improve the overall benefits provided by
   fine wool sheep [[62]28]. Exploring the developmental characteristics
   of IMF deposition and selecting candidate genes for AFWS provide
   references for future studies and applications in sheep breeding,