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MicroRNA expression profiles differ between primary myofiber of lean and obese pig breeds
Dongting He1, Tiande Zou1, Xiangrong Gai2
1Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China.
Abstract:
MicroRNAs (miRNAs) are non-coding small miRNAs ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and these differences are programmed during prenatal muscle development. Little research shed light directly on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. Myofiber phenotypes of LW and MS were measured at developmental stages of 35, 55 and 90 days post-conception (dpc), which revealed that the myogenesis process is more intense in MS than in LW at 35 dpc. To investigate the role of miRNAs involved in regulating muscle development at earlier stages of myogenesis and decipher the miRNAs transcriptome difference between LW and MS, here, the miRNAomes of longissimus dorsi muscle collected at 35 dpc from female LW and MS were analyzed by deep sequencing. Overall, 1147 unique miRNAs comprising 434 known miRNAs, 239 conserved miRNAs and 474 candidate miRNAs were identified. Expression analysis of the 10 most abundant miRNAs in every library indicated that functional miRNAome may be a small amount and tend to be greater expressed. These sets of miRNA may play house keeping roles that were involved in myogenesis. A total of 87 miRNAs were significantly differentially expressed between LW and MS (reads > 1000, P < 0.05). Gene ontology (GO) and KEGG pathway enrichment analysis revealed that the differentially expressed miRNAs (DE miRNAs) were associated mainly with muscle contraction, WNT, mTOR, and MAPK signaling pathways. Some myogenesis related miRNAs (miR-133, miR-1, miR-206 and miR-148a) are highly abundant in MS, while other miRNAs (let-7 family, miR-214, miR-181) highly expressed in LW. In addition, the expression patterns of miRNAs (miR-1, -133, -206) at three prenatal stages (35, 55 and 90 dpc) were determined using qRT-PCR. Notably, ssc-miR-133 was significantly more highly expressed in LW pigs skeletal muscle at all prenatal stages compared with its expression in LW pigs skeletal muscle. Taken together, the main functional miRNAs during muscle development are different between lean and obese pig breeds. The present study adds new information to existing data on porcine miRNAs and will be helpful to investigate the dominant (main functional) muscle-related miRNAs sets in different pig breeds.
Insights
Lean and obese pig breeds exhibit distinct prenatal muscle microRNA (miRNA) expression profiles. These differences in muscle-specific miRNAs are linked to variations in myogenesis and muscle development, impacting meat quality.
Area of Science:
- Animal Genetics
- Molecular Biology
- Developmental Biology
Background:
- MicroRNAs (miRNAs) are key regulators of gene expression, crucial for muscle development.
- Significant phenotypic differences exist between Large White (lean) and Meishan (obese) pigs, originating during prenatal development.
- Limited research has directly compared miRNA transcriptomes in prenatal muscle between these distinct pig breeds.
Purpose of the Study:
- To investigate miRNA transcriptome differences in prenatal longissimus dorsi muscle between Large White and Meishan pigs.
- To identify key miRNAs involved in regulating prenatal myogenesis in these breeds.
- To understand the role of specific miRNAs in programming postnatal muscle growth and meat quality differences.
Main Methods:
- Deep sequencing of miRNAomes from longissimus dorsi muscle at 35 days post-conception (dpc) in female pigs.
- Bioinformatic analysis to identify known, conserved, and novel miRNAs.
- Differential expression analysis and Gene Ontology (GO) / KEGG pathway enrichment analysis.
- Quantitative reverse transcription PCR (qRT-PCR) validation of specific miRNA expression patterns at 35, 55, and 90 dpc.
Main Results:
- 1147 unique miRNAs were identified, with a subset of highly expressed miRNAs potentially playing housekeeping roles in myogenesis.
- 87 miRNAs were significantly differentially expressed between Large White and Meishan pigs.
- Differentially expressed miRNAs were associated with muscle contraction and signaling pathways (WNT, mTOR, MAPK).
- Specific myogenesis-related miRNAs (e.g., miR-133, miR-1, miR-206) showed higher abundance in Meishan pigs, while others (let-7 family, miR-214) were higher in Large White pigs.
- ssc-miR-133 showed significantly higher expression in Large White pigs across all prenatal stages studied.
Conclusions:
- Distinct sets of functional miRNAs are involved in muscle development between lean (Large White) and obese (Meishan) pig breeds.
- These miRNA differences likely contribute to the programmed variations in myogenesis and subsequent muscle characteristics.
- The study provides valuable insights into breed-specific muscle-related miRNAs, aiding future research on porcine muscle development and meat quality.
