title: High-throughput sequencing as an effective approach in profiling small RNAs derived from a hairpin RNA expression vector in woody plants.
abstract: Hairpin RNA (hpRNA)-mediated gene silencing has proved to be an efficient approach to develop virus-resistant transgenic plants. To characterize small RNA molecules (sRNAs) derived from an hpRNA expression vector in transgenic cherry rootstock plants, we conducted small RNA sequencing of (1) a transgenic rootstock containing an inverted repeat of the partial coat protein of Prunus necrotic ring spot virus (PNRSV-hpRNA); (2) a nontransgenic rootstock; and (3) a PNRSV-infected sweet cherry plant. Analysis of the PNRSV sRNA pools indicated that 24-nt (nucleotide) small interfering RNAs (siRNAs) were the most prevalent sRNAs in the transgenic rootstock whereas the most abundant sRNAs in the PNRSV-infected nontransgenic rootstock were 21-nt siRNAs. In addition, the 24-nt siRNAs of the PNRSV-hpRNA were more abundant on the sense strand than those on the antisense strand in the transgenic rootstock. In contrast, preference in generating PNRSV sRNAs, ranging from 19-nt to 30-nt for sense and antisense strands, was not distinct in the PNRSV-infected nontransgenic sweet cherry. Taken together, this is the first report on profiling hpRNA-derived sRNAs in woody plants using high-throughput sequencing technology, which is an efficient way to verify the presence/absence, the abundance, and the sequence features of certain sRNAs.
authors.affiliation: Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA. Electronic address: zhaodon4@msu.edu.
authors.forename: Dongyan
authors.initials: D
authors.lastname: Zhao
authors.affiliation: Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA. Electronic address: songg@msu.edu.
authors.forename: Guo-Qing
authors.initials: GQ
authors.lastname: Song
mesh_terms: D015152:Blotting, Northern; D020869:Gene Expression Profiling / Q000379:methods*; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D018517:Plant Roots / Q000378:metabolism; D010942:Plant Viruses / Q000502:physiology; D030821:Plants, Genetically Modified / Q000378:metabolism; D027861:Prunus / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012313:RNA
keywords: Cherry; RNAi; Small interfering RNAs; Transgenic woody plant; Virus resistance