Comparative Profiling of microRNA Expression in Soybean Seeds from Genetically Modified Plants and their Near-Isogenic Parental Lines

<div><p>MicroRNAs (miRNAs) have been widely demonstrated to play fundamental roles in gene regulation in most eukaryotes. To date, there has been no study describing the miRNA composition in genetically modified organisms (GMOs). In this study, small RNAs from dry seeds of two GM soybean lines and their parental cultivars were investigated using deep sequencing technology and bioinformatic approaches. As a result, several differentially expressed gma-miRNAs were found between the GM and non-GM soybeans. Meanwhile, more differentially expressed gma-miRNAs were identified between distantly relatednon-GM soybeans, indicating that the miRNA components of soybean seeds varied among different soybean lines, including the GM and non-GM soybeans, and the extent of difference might be related to their genetic relationship. Additionally, fourteen novel gma-miRNA candidates were predicted in soybean seeds including a potential bidirectionally transcribed miRNA family with two genomic loci (gma-miR-N1). Our findings firstly provided useful data for miRNA composition in edible GM crops and also provided valuable information for soybean miRNA research.</p></div

Verification of differentially expressed gma-miRNAs by quantitative RT-PCR.

<p>Identical primers were designed for similar mature miRNAs. The comparative ΔΔCT method was used for the quantitative RT-PCR experiments and the U6 snRNA was selected as the reference gene. A: Results of the comparison between MON89788 and A3244. B: Results of the comparison between DP-3Ø5423×GTS 40-3-2 and Jack.</p

Novel gma-miRNA candidates found in this study.

<p>A: Hairpin structures of novel gma-miRNA precursors predicted in GM soybean seeds. Mature miRNAs are indicated with red lowercase letters. B: Expression analysis of novel gma-miRNA candidates by RT-PCR. NTC, no template control; MON, MON89788; A32, A3244; DP3, DP-3Ø5423×GTS 40-3-2; JAC, Jack.</p

Results of novel gma-miRNA prediction in soybean seeds.

<p>Results of novel gma-miRNA prediction in soybean seeds.</p

Length distribution and Venn diagram of small RNA libraries.

<p>A: Length distribution of the unique reads. B: Length distribution of the total reads. C: Venn diagram of four small RNA libraries. All of the small RNA reads from four libraries are combined as whole. Each percentage is calculated by dividing the number of reads in each library. U, unique; T, total; MON, MON89788; A32, A3244; DP3, DP-3Ø5423×GTS 40-3-2; JAC, Jack.</p

Composition of small RNA libraries from soybean seeds of GM and their parental lines.

<p>Composition of small RNA libraries from soybean seeds of GM and their parental lines.</p