Identification of miRNAs and their targets in transgenic Brassica napus and its acceptor (Westar) by high-throughput sequencing and degradome analysis

MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that play many roles in plant growth, development, and the stress response. Recently, the Brassica napus (B. napus) genome was reported, which allows the genome-wide identification of miRNAs and their targets in B. napus cv. Westar and its transgenic cultivar. Thus, two sRNAs libraries and two degradome libraries of the transgenic B. napus (TG) and its acceptor (B. napus cv. Westar, WA) were constructed. Following high-throughput sequencing and miRNA identification, 139 unique conserved and 305 unique novel miRNA sequences were identified in the two sRNA libraries, and through degradome analysis, 540 targets corresponding to 167 unique miRNA sequences were identified in the two degradome libraries. 11 differentially expressed unique miRNA sequences were verified by quantitative real-time PCR (qRT-PCR), and the results nearly agreed with the high-throughput sequencing data. The present study increases the number of miRNAs identified in B. napus and suggests that there are possible differences in the miRNA expression between transgenic B. napus and its acceptor.