title: Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.).
abstract: Phosphorus is one of the major factors controlling plant growth and productivity. Although physiological and molecular processes of P deficiency have been intensively investigated, our current understanding of the coordinated regulation of phosphate-responsive genes and signal networks is limited. In the present study, we performed a microarray-based genome-wide transcriptional analysis of miRNAs from soybean (Glycine max L.) under phosphate deficiency. miRNAs extracted from P-deficient and P-sufficient soybean were hybridized to an array containing 853 known plant miRNA sequences. An induction ratio significant at p<0.01 was observed for 57 miRNAs belonging to 27 families. Among these miRNA families, which differentially expressed, 7 and 8 were found to be up-regulated, whereas 17 and 6 were down-regulated in leaves and roots, respectively. Seven representative individual miRNAs were selected for qRT-PCR validation, and most showed an expression pattern similar to that on microarray. We further predicted P-responsive cis-elements from the promoters of miRNAs in response to and non-responding to P deficiency. In total, 125 putative cis-elements were identified for 24 soybean P-deficient responsive miRNAs. Interestingly, those miRNAs (54) not responding to P deficiency were also found to contain the same P-responsive motifs. A comparative analysis revealed that the frequency of the motif occurrence in the promoters of miRNA genes in response to P deficiency was higher than that of miRNA genes not responding to P deficiency. Our study provides initial evidence in soybean that a set of miRNAs with a high frequency of P-responsive cis-elements may coordinately regulate the plant response to P deficiency.
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Tong Wen Road 1, Nanjing 210095, China.
authors.forename: Hou Qing
authors.initials: HQ
authors.lastname: Zeng
authors.forename: Yi Yong
authors.initials: YY
authors.lastname: Zhu
authors.forename: Si Qi
authors.initials: SQ
authors.lastname: Huang
authors.forename: Zhi Min
authors.initials: ZM
authors.lastname: Yang
mesh_terms: D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010758:Phosphorus / Q000172:deficiency* / Q000494:pharmacology; D011401:Promoter Regions, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D015203:Reproducibility of Results; D013025:Glycine max / Q000187:drug effects / Q000235:genetics*; D016385:TATA Box / Q000235:genetics; D024363:Transcription Initiation Site
chemical_list: D035683:MicroRNAs; D010758:Phosphorus