He Dongting, Zou Tiande, Gai Xiangrong, Ma Jideng, Li Mingzhou, Huang Zhiqing, Chen Daiwen
Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China.
State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, People's Republic of China.
PLoS One. 2017 Jul 31;12(7):e0181897. doi: 10.1371/journal.pone.0181897. eCollection 2017.
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.
微小RNA（miRNA）是长度约为22个核苷酸的非编码小RNA，通过与信使RNA（mRNA）结合在肌肉发育中发挥重要作用。大白猪（LW，瘦肉型猪）和梅山猪（MS，中国本土肥胖品种）在生长速度、肌肉量和肉质方面具有显著的出生后表型差异，这些差异在产前肌肉发育过程中就已编程。很少有研究直接揭示这两个不同猪品种产前肌肉中miRNA转录组的差异。在受孕后35、55和90天（dpc）的发育阶段测量了LW和MS的肌纤维表型，结果显示在35 dpc时，MS的肌生成过程比LW更强烈。为了研究miRNA在肌生成早期阶段调节肌肉发育中的作用，并破译LW和MS之间的miRNA转录组差异，在此，通过深度测序分析了从雌性LW和MS在35 dpc收集的背最长肌的miRNA组。总体而言，共鉴定出1147个独特的miRNA，包括434个已知miRNA、239个保守miRNA和474个候选miRNA。对每个文库中10个最丰富的miRNA进行表达分析表明，功能性miRNA组可能数量较少且倾向于更高表达。这些miRNA组可能发挥参与肌生成的看家作用。LW和MS之间共有87个miRNA显著差异表达（reads > 1000，P < 0.05）。基因本体（GO）和KEGG通路富集分析表明，差异表达的miRNA（DE miRNA）主要与肌肉收缩、WNT、mTOR和MAPK信号通路相关。一些与肌生成相关的miRNA（miR-133、miR-1、miR-206和miR-148a）在MS中高度丰富，而其他miRNA（let-7家族、miR-214、miR-181）在LW中高度表达。此外，使用qRT-PCR确定了miRNA（miR-1、-133、-206）在三个产前阶段（35、55和90 dpc）的表达模式。值得注意的是，与LW猪骨骼肌中的表达相比，ssc-miR-133在所有产前阶段的LW猪骨骼肌中显著更高表达。综上所述，瘦肉型和肥胖型猪品种在肌肉发育过程中的主要功能性miRNA不同。本研究为猪miRNA的现有数据增添了新信息，将有助于研究不同猪品种中主要的（主要功能性）肌肉相关miRNA组。
