Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
BMC Genomics. 2022 Apr 11;23(1):294. doi: 10.1186/s12864-022-08515-7.
Long-term artificial selection for growth rate and lean meat rate has eventually led to meat quality deterioration. Muscle fiber type is a key factor that markedly affects meat quality. circRNAs have been reported to participate in diverse biological activities, including myofiber growth and development; thus, we herein compared porcine circRNA transcriptome between oxidative and glycolytic muscle tissues.
Longissimus thoracis muscle tissues were obtained from Lantang and Landrace pigs at birth (LT1D and LW1D, respectively) and 90 postnatal days (LT90D and LW90D, respectively). Hematoxylin and eosin staining and quantitative real-time PCR revealed that all structural traits of the muscle showed large variations between different breeds and growth stages. In total, 329 known miRNAs and 42,081 transcript candidates were identified; 6,962 differentially expressed transcripts were found to play a key role in myogenesis by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In addition, 3,352 circRNAs were identified using five predicting algorithms, and 104 circRNA candidates were differentially expressed. Integrated analysis of differentially expressed miRNAs, mRNAs, and circRNAs led to the identification of 777, 855, and 22 convincing ceRNA interactions in LT1D vs. LT90D, LW1D vs. LW90D, and LT90D vs. LW90D, respectively. Finally, we identified a circRNA candidate circKANSL1L, which showed high homology between mice and pigs, and it was found to inhibit the proliferation of CC cells but promote their differentiation.
We identified genome-wide circRNAs in 0- and 90-day-old Lantang and Landrace pigs by RNA-seq and found that circRNAs were abundant, differentially expressed, and associated with myogenesis. Our results should serve as a reference for future studies on pork quality.
长期以来，为了提高生长速度和瘦肉率而进行的人工选择，最终导致了肉质的恶化。肌纤维类型是显著影响肉质的关键因素。circRNAs 已被报道参与多种生物学活动，包括肌纤维的生长和发育；因此，我们在此比较了氧化型和糖酵解型肌肉组织之间的猪 circRNA 转录组。
分别在出生时（LT1D 和 LW1D）和 90 日龄时（LT90D 和 LW90D）从蓝塘猪和长白猪的背最长肌组织中提取了组织样本。苏木精-伊红染色和定量实时 PCR 显示，不同品种和生长阶段的肌肉结构特征均有较大差异。总共鉴定出 329 个已知的 miRNA 和 42081 个转录本候选物；通过基因本体和京都基因与基因组百科全书通路分析，发现 6962 个差异表达的转录本在肌生成中起关键作用。此外，使用 5 种预测算法鉴定出 3352 个 circRNAs，其中 104 个 circRNA 候选物差异表达。差异表达的 miRNA、mRNA 和 circRNA 的综合分析分别在 LT1D 与 LT90D、LW1D 与 LW90D、LT90D 与 LW90D 之间鉴定出 777、855 和 22 个可信的 ceRNA 相互作用。最后，我们鉴定出一个 circRNA 候选物 circKANSL1L，它在小鼠和猪之间具有高度同源性，发现它能抑制 CC 细胞的增殖，但促进其分化。
我们通过 RNA-seq 鉴定了 0 日龄和 90 日龄蓝塘猪和长白猪的全基因组 circRNAs，发现 circRNAs 丰富、差异表达，并与肌生成有关。我们的研究结果为未来的猪肉质量研究提供了参考。
