Small RNA Regulation in Barley under Different Phosphorous Conditions

Barley (Hordeum vulagre L.) is one of the most important cereal crops worldwide and phosphorus (P) is an essential nutrient for plant growth and development. In this study, we analysed next generation sequencing small RNA (sRNA) datasets from barley grown under P-sufficient and P-deficient conditions. We found that many classes of sRNAs, such as microRNAs (miRNAs), sense and antisense sRNAs, repeat-associated sRNAs, tRNA-derived sRNAs and chloroplast-derived sRNAs, were significantly differentially expressed between the two P conditions, indicating their involvements in P uptake into the plants. The most abundant sRNA class identified in both P conditions is antisense sRNAs. In addition, about one fourth of sRNAs were derived from the chloroplast genome and a chloroplast-encoded tRNA-derived sRNA was the most abundant sRNA of all the sRNAs sequenced. A total of 233 miRNAs were identified, of which 55 were only present under P-deficient condition, 32 uniquely existed under P-sufficient condition, and 47 were significantly differentially expressed between the two P conditions (|log₂|>1). miR399 and miR827 were the two most significantly up-regulated miRNAs under P-deficient condition. miR399 and miR827 are both involved in conserved P deficiency signalling pathways. miR399 targets the PHO2 gene encoding E2 enzyme that negatively regulates phosphate uptake and root-to-shoot allocation, while miR827 targets SPX-domain-containing genes that negatively regulate other P-responsive genes. Some isomirs of miR399 and miR827 were also identified to be up-regulated under P-deficient condition. Surprisingly, a few sRNAs derived from the single-stranded loops of pre-miR399s were found and functional. It is unclear how these loop-derived sRNAs were generated. Our data provide important insights into the potential roles of sRNAs in the control of phosphate homeostasis.