Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs

Abstract

Intramuscular fat (IMF) content is closely related to various meat traits, such as tenderness, juiciness, and flavor. The IMF content varies considerably among pig breeds with different genetic backgrounds. Long intergenic non-coding RNAs (lincRNAs) have been widely identified in many species and found to be an important class of regulators that can participate in multiple biological processes. However, the mechanism behind lincRNAs regulation of pig IMF content remains unknown and requires further study. In our study, we identified a total of 156 lincRNAs in the longissimus dorsi muscle of Wei (fat-type) and Yorkshire (lean-type) pigs using previously published data. These identified lincRNAs have shorter transcript length, longer exon length, lower exon number, and lower expression level as compared with protein-coding transcripts. We predicted potential target genes (PTGs) that are potentially regulated by lincRNAs in cis or trans regulation. Gene ontology and pathway analyses indicated that many potential lincRNAs target genes are involved in IMF-related processes or pathways, such as fatty acid catabolic process and adipocytokine signaling pathway. In addition, we analyzed quantitative trait locus (QTL) sites that differentially expressed lincRNAs (DE lincRNAs) between Wei and Yorkshire pigs co-localized. The QTL sites where DE lincRNAs co-localize are mostly related to IMF content. Furthermore, we constructed a co-expressed network between DE lincRNAs and their differentially expressed PTGs (DEPTGs). On the basis of their expression levels, we suggest that many DE lincRNAs can affect IMF development by positively or negatively regulating their PTGs. This study identified and analyzed some lincRNAs- and PTGs-related IMF development of the two pig breeds and provided new insight into research on the roles of lincRNAs in the two types of breeds.

IRLnc: A novel functional noncoding RNA contributes to intramuscular fat deposition

“…And other genes were mainly associated with diseases such as Mucopolysaccharidosis IIIB [23], stress-induced injury [24], oral-facial-digital syndromes [25], and breast cancer [26]. From the results, intramuscular related genes involved in fat and muscle related function were consistent with previous research, which reported that IMF is regulated through a complex pathway that interacts with muscle, fat, and connective tissue [27,28].…”

IRLnc: A novel functional noncoding RNA contributes to intramuscular fat deposition

“…And other genes were mainly associated with diseases such as Mucopolysaccharidosis IIIB [29], stress-induced injury [30], oral-facial-digital syndromes [31], and breast cancer [32]. From the results, intramuscular related genes involved in fat and muscle related function were consistent with previous research, which reported that IMF is regulated through a complex pathway that interacts with muscle, fat, and connective tissue [33,34].…”

Muscle Transcriptome Analysis Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Pigs

“…Several studies on transcriptome profiling of porcine longissimus dorsi (LD) have been performed to investigate genes or pathways influencing IMF content in pigs. However, most of these studies have been carried out using pigs of different breeds ( Li et al, 2016 , 2020 ; Xu J. et al, 2018 ), with few studies on individuals of the same breed ( Lim et al, 2017 ; Muñoz et al, 2018 ) with distinct IMF content to identify consistent candidate genes. Hence, based on the RNA-seq, further studies using multiple analysis methods should be conducted to unravel genes and the pathways that regulate IMF contents.…”