title: MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity.
abstract: *MicroRNAs (miRNAs) play a pivotal role in post-transcriptional regulation of gene expression in plants. Information on miRNAs in legumes is as yet scarce. This work investigates miRNAs in an agronomically important legume, common bean (Phaseolus vulgaris). *A hybridization approach employing miRNA macroarrays - printed with oligonucleotides complementary to 68 known miRNAs - was used to detect miRNAs in the leaves, roots and nodules of control and nutrient-stressed (phosphorus, nitrogen, or iron deficiency; acidic pH; and manganese toxicity) common bean plants. *Thirty-three miRNAs were expressed in control plants and another five were only expressed under stress conditions. The miRNA expression ratios (stress:control) were evaluated using principal component and hierarchical cluster analyses. A group of miRNAs responded to nearly all stresses in the three organs analyzed. Other miRNAs showed organ-specific responses. Most of the nodule-responsive miRNAs showed up-regulation. miRNA blot expression analysis confirmed the macroarray results. Novel miRNA target genes were proposed for common bean and the expression of selected targets was evaluated by quantitative reverse transcriptase-polymerase chain reaction. *In addition to the detection of previously reported stress-responsive miRNAs, we discovered novel common bean stress-responsive miRNAs, for manganese toxicity. Our data provide a foundation for evaluating the individual roles of miRNAs in common bean.
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México.
authors.forename: Oswaldo
authors.initials: O
authors.lastname: Valdés-López
authors.forename: S Samuel
authors.initials: SS
authors.lastname: Yang
authors.forename: Rosaura
authors.initials: R
authors.lastname: Aparicio-Fabre
authors.forename: Peter H
authors.initials: PH
authors.lastname: Graham
authors.forename: José Luis
authors.initials: JL
authors.lastname: Reyes
authors.forename: Carroll P
authors.initials: CP
authors.lastname: Vance
authors.forename: Georgina
authors.initials: G
authors.lastname: Hernández
mesh_terms: D018533:Biomass; D015152:Blotting, Northern; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D008345:Manganese / Q000633:toxicity*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D027805:Phaseolus / Q000187:drug effects / Q000235:genetics*; D010641:Phenotype; D025341:Principal Component Analysis; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D013054:Spectrophotometry, Atomic; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D008345:Manganese