Abstract：miRNA plays an important role in sheep (Ovis aries) skeletal muscle development. This study aimed to find out the differently expressed miRNA in Bashbay sheep skeletal muscle during different development stages, and to furtherly understand the relationship between miRNA expression and excellent meat traits of Bashbay sheep. In this study, the Solexa sequencing technology was applied to investigate the miRNA expressing profiles in Bashbay sheep skeletal muscle during fetal period (mixed sample of 40, 50, 60, 80, 100 and 120 d) and postnatal stage (mixed sample of newborn, 30, 60 and 90 d). By high-throughput sequencing and data analysis, 11.82 M and 11.51 M clean reads, and 0.31 M 0.28 M unique sequences were obtained. Among them, 20% and 17% were candidate miRNA sequences, respectively. Then blastn was performed between miRBase (V21.0) and unique sequences, and finally got 537 and 496 miRNAs which were conservative among species. There were 102 and 115 miRNAs of them were matched with ovine known miRNAs, respectively. The rest sequences were compared with EST database of sheep, and 486 and 510 new candidate miRNAs were obtained by Mfold and MiPred program. There were total 385 miRNAs which differently expressed between fetal and postnatal skeletal muscle of Bashbay sheep (expressing change were above 2 fold), including 203 up-regulated and 182 down-regulated miRNAs, respectively. Applying TargetScan, Pictar and miRanda, the candidate target genes of top 10 up- and down-regulated miRNAs were predicted, and the one which was predicted by at least two programs was chosen to be further analyzed. Total 3 852 candidate target genes were predicted, and most of them participated in many important signal pathways, just like mitogen-activated protein kinases (MAPK), wingless type MMTV (mouse mammary tumor virus) integration site family members (WNT) and adherens junction, etc. This study enriches the miRNA database of sheep skeletal muscle, and could help to further understand the regulation mechanism of miRNA in sheep skeletal muscle development.
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