RNA silencing as a tool to uncover gene function and engineer novel traits in soybean

Abstract

RNA silencing refers collectively to diverse RNA-mediated pathways of nucleotide-sequence-specific inhibition of gene expression. It has been used to analyze gene function and engineer novel traits in various organisms. Here, we review the application of RNA silencing in soybean. To produce soybean lines, in which a particular gene is stably silenced, researchers have frequently used a transgene that transcribes inverted repeats of a target gene segment. Suppression of gene expression in developing soybean embryos has been one of the main focuses of metabolic engineering using transgene-induced silencing. Plants that have enhanced resistance against diseases caused by viruses or cyst nematode have also been produced. Meanwhile, Agrobacterium rhizogenes-mediated transformation has been used to induce RNA silencing in roots, which enabled analysis of the roles of gene products in nodulation or disease resistance. RNA silencing has also been induced using viral vectors, which is particularly useful for gene function analysis. So far, three viral vectors for virus-induced gene silencing have been developed for soybean. One of the features of the soybean genome is the presence of a large number of duplicated genes. Potential use of RNA silencing technology in combination with forward genetic approaches for analyzing duplicated genes is discussed.

Keywords: RNA interference; epigenetic changes; metabolic engineering; post-transcriptional gene silencing; soybean (Glycine max); transgene; virus-induced gene silencing.

Fig. 1

Pathways of RNA silencing used to engineer novel traits in plants. Posttranscriptional gene silencing is triggered by dsRNA. Transcripts from transgenes that have an IR sequence can form dsRNA. Sense transcripts can produce dsRNA through the synthesis of complementary strand by RdRP. The replication intermediate or duplex structures formed within single-stranded RNA of the viral genome can also provide dsRNA. These dsRNAs are processed into siRNAs by the endonuclease Dicer. The siRNA is loaded into the RISC complex that contains AGO and guides the RISC complex to the mRNA by base-pairing. The RISC complex cuts the mRNA, which is subsequently degraded. siRNA can also induce epigenetic changes involving DNA methylation and/or changes in histone modification in the nucleus. These changes can convert nucleosomes to a more tightly packed structure, thereby transcription is repressed. Abbreviations: IR, inverted repeat; RdRP, RNA-dependent RNA polymerase; dsRNA, double-stranded RNA; siRNA, short interfering RNA; RISC, RNA-induced silencing complex; AGO, Argonaute.