Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences...

Area of Science:

• Animal Genetics
• Molecular Biology
• Meat Science

Background:

• Intramuscular fat (IMF) significantly influences meat quality traits like tenderness, juiciness, and flavor.
• IMF content exhibits considerable variation across pig breeds due to differing genetic backgrounds.
• Long intergenic non-coding RNAs (lincRNAs) are emerging as crucial regulators in diverse biological processes, but their role in pig IMF regulation is largely unexplored.

Purpose of the Study:

• To identify and characterize lincRNAs involved in regulating intramuscular fat (IMF) content in different pig breeds.
• To elucidate the regulatory mechanisms of lincRNAs in IMF development.
• To provide novel insights into the genetic basis of meat quality traits in pigs.

Main Methods:

• Identification of 156 lincRNAs in the longissimus dorsi muscle of fat-type (Wei) and lean-type (Yorkshire) pigs.
• Prediction of potential target genes (PTGs) for identified lincRNAs using cis and trans regulation analysis.
• Gene ontology and pathway analyses to determine the involvement of PTGs in IMF-related biological processes.
• Analysis of quantitative trait loci (QTL) co-localization with differentially expressed lincRNAs (DE lincRNAs).
• Construction of a co-expression network between DE lincRNAs and their differentially expressed PTGs (DEPTGs).

Main Results:

• Identified 156 lincRNAs with distinct characteristics (shorter transcript length, longer exon length, lower exon number, and lower expression) compared to protein-coding transcripts.
• Gene ontology and pathway analyses revealed that PTGs are significantly enriched in IMF-related processes, including fatty acid catabolism and adipocytokine signaling.
• DE lincRNAs significantly co-localized with QTLs associated with IMF content.
• A co-expression network highlighted potential positive and negative regulatory roles of DE lincRNAs on their DEPTGs in IMF development.

Conclusions:

• This study successfully identified and analyzed lincRNAs and their target genes associated with intramuscular fat (IMF) development in Wei and Yorkshire pigs.
• The findings suggest that lincRNAs play a significant role in regulating IMF content by modulating the expression of target genes.
• This research provides a foundation for understanding the function of lincRNAs in meat quality traits and offers new avenues for genetic improvement in pigs.