Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education and Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, P.R. China.
Swine Breeding Quality Supervision and Inspection Center of the Ministry of Agriculture (Wuhan), Huazhong Agricultural University, Wuhan, P.R. China.
PLoS One. 2018 Jul 11;13(7):e0200445. doi: 10.1371/journal.pone.0200445. eCollection 2018.
Tongcheng (TC) and Yorkshire (YK) are two pig breeds with distinctive muscle morphology. Porcine microRNAome (miRNAome) of the longissimus muscle during five developmental stages (40, 55, 63, 70, and 90 days post coitum (dpc)) was explored by Solexa sequencing in the present study to find miRNAs involved in the different regulation of skeletal muscle development between the two breeds. A total of 320 known porcine miRNAs, 64 miRNAs corresponding to other mammals, and 224 potentially novel miRNAs were identified. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) suggested that the factor "pig breed" affected the miRNA expression profiles to a lesser extent than the factor "developmental stage". Fifty-seven miRNAs were differentially expressed (DE) between the neighbor developmental stages in TC and 45 such miRNAs were found in YK, 34 in common; there were more down-regulated stage-DE miRNAs than up-regulated. And a total of 23, 30, 12, 6, and 30 breed-DE miRNAs between TC and YK were identified at 40, 55, 63, 70, and 90 dpc, respectively, which were mainly involved in cellular protein modification process, protein transport, and metabolic process. As the only highly expressed breed-DE miRNA found in no less than four developmental stages, and also a stage-DE miRNA found both in TC and YK, miR-499-5p could bind the 3'-UTR of a myofibrillogenesis regulator, destrin/actin depolymerizing factor (DSTN), as validated in dual luciferase reporter assay. The results suggested that miR-499-5p possibly play a noteworthy role in the breed-distinctive porcine muscle fiber development associated with the regulation of DSTN.
桐城（TC）和约克夏（YK）是两种具有不同肌肉形态的猪品种。本研究通过 Solexa 测序技术研究了这两个品种在五个发育阶段（受精后 40、55、63、70 和 90 天）的背最长肌中的猪 microRNA 组（miRNAome），以寻找参与两种品种骨骼肌肉发育不同调控的 miRNA。共鉴定出 320 个已知的猪 miRNA、64 个对应于其他哺乳动物的 miRNA 和 224 个潜在的新 miRNA。主成分分析（PCA）和层次聚类分析（HCA）表明，“猪品种”因素对 miRNA 表达谱的影响小于“发育阶段”因素。在 TC 中，57 个 miRNA 在相邻发育阶段之间存在差异表达（DE），而在 YK 中则发现了 45 个这样的 miRNA，其中 34 个是共同的；下调的阶段 DE miRNA 多于上调的。在 TC 和 YK 之间，分别在 40、55、63、70 和 90 dpc 时鉴定出 23、30、12、6 和 30 个品种 DE miRNA，主要涉及细胞蛋白修饰过程、蛋白质转运和代谢过程。miR-499-5p 是唯一在不少于四个发育阶段高度表达的品种 DE miRNA，也是在 TC 和 YK 中均发现的阶段 DE miRNA，如双荧光素酶报告基因检测所验证的，它可以与肌原纤维生成调节剂、肌动蛋白解聚因子（DSTN）的 3'-UTR 结合。结果表明，miR-499-5p 可能在与 DSTN 调控相关的品种特异性猪肌肉纤维发育中发挥重要作用。
