Identification of MicroRNAs Associated with Nitrogen Use Efficiency and Fertility in Rice

• Published in: International journal of agriculture and biology 2015-12, Vol.17 (6), p.1231-1236
• Main Authors: Ouyang, Jie-xiu, Li, Shao-bo
• Format: Article
• Language: English
• ISSN: 1560-8530; 1814-9596
• DOI: 10.17957/IJAB/14.0037

A study was conducted to identify target genes through differential expression of microRNAs (miRNAs) under low nitrogen (low-N) level (0.01 mM NH4NO3) for tolerant and sensitive rice samples, which may provide valuable information for breeding and improving production under nitrogen stress condition. MiRNA microarray data GSE38213 were downloaded from Gene Expression Ominibus database, including 2 low-N tolerant rice samples and 2 low-N sensitive rice samples. After the data were preprocessed and normalized, limma package in R was applied to identify the differentially expressed miRNAs. Then the target genes of the most significant up-regulated miRNAs were collected by using Plant miRNA Database. In addition, the high-reliable signal nucleotide polymorphisms (SNPs) of target genes were screened out by Rice Genome Browser in TIFR (The Institute for Genomic Research). Functional analysis was performed to the genes with SNPs. As the results, total 22 differentially expressed miRNAs were identified and the most significant ones were osa-miR530-3p, and osa-miR319a. Additionally, high-reliable SNPs were only discovered in 4 target genes of osa-miR530-3p. Functional analysis revealed that the 4 target genes of osa-miR530-3p were associated with plant growth, development and respiration. In conclusion, differentially expressed osa-miR530-3p and its target genes that had high-reliable SNPs were identified in present study. Besides, miR167 and miR319 were found to be associated with fertility. These miRNAs identified in the present study are potential targets for developing high yield low-N tolerant rice. Copyright 2014 Friends Science Publishers