Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology

microRNAs (miRNAs) perform critical roles in various biological and metabolic processes by regulating gene expression at the post-transcriptional level. To investigate the functional roles of miRNAs in the lactating mammary gland of Capra hircus, a library was constructed from the lactating mammary glands of Laoshan dairy goats (C. hircus) during early lactation. The miRNA expression profiles were systematically screened, and miRNAs were identified and characterized using Solexa deep-sequencing technology and bioinformatics. As a result, a total of 18,031,615 clean reads were obtained representing 305,711 unique sRNAs. A total of 12,086,616 sRNAs representing 3,701 unique sRNAs matched the known Bos taurus miRNA precursors in miRBase 17.0, and 300 known miRNAs and 15 miRNA* were discovered. In addition, 131 novel miRNAs sequences were also obtained, and 147,703 putative targets were predicted. GO and KEGG pathway analysis showed that the majority of targets were involved in cellular processes and metabolic pathways. The 290 known miRNAs, 14 miRNA* and 38 novel miRNAs were validated by sequencing a second library that was constructed from the same tissues as the first library. Our study provided the first large-scale identification and characterization of miRNAs in the mammary gland tissue of the dairy goat. The results indicate that the regulation of miRNA-mediated gene expression occurs during early lactation in dairy goats. This study significantly enriches the C. hircus miRNA repertoire and provides a reference for the elucidation of complex miRNA-mediated regulatory networks for gene expression in the physiology and developmental progression of the lactating mammary gland.