ARS | Publication request: microRNAs and microRNA Targets Involved in Alfalfa Stem Development

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 9, 2009
Publication Date: January 9, 2010
Citation: Valdes-Lopez, O., Yang, S.H., Foo, C., Gronwald, J.W., Samac, D.A., Hernandez, G., Vance, C.P. 2010. microRNAs and microRNA Targets Involved in Alfalfa Stem Development [abstract]. XVIII Plant and Animal Genome Conference Proceedings, January 9-13, 2010, San Diego, California. Abstract P727.

Technical Abstract: To examine the possible involvement of microRNAs in alfalfa stem development, we hybridized 32P-labled total microRNAs purified from elongating and post-elongation stem internodes (ES and PES, respectively) of the alfalfa Clone 252 to a microRNA dot blot that contains a total of 70 reference anti-miRNA oligonucleotides from Arabidopsis thaliana, Phaseolus vulgaris (common bean), and Glycine max (soybean). After three independent hybridizations, the signal for each microRNA was normalized using the microRNA pvu-miR482 signal as a control (normalization = signal/control). Using a t-test with p-value cut-off of 0.05, we identified four microRNAs up-regulated and one down-regulated in PES compared to ES. We also identified six microRNAs detected only in PES and two of them were involved in the auxin signaling. To predict the global expression pattern of microRNAs and microRNA target genes during alfalfa stem development, the 266 putative Medicago microRNAs currently available in Medicago-MIRATdb were used to search putative targets among Medicago GeneChip probe set consensus sequences using the psRNATarget algorithm. A total of 1,318 putative microRNA target probe sets were identified. Fisher's exact test with Bonferroni correction identified over-representation of genes involved in photosynthesis, amino acid metabolism, stress response, and transcription factors among putative microRNA targets. The expression pattern of putative microRNA target genes in the alfalfa stem GeneChip data (ES vs. PES and alfalfa Clones 252 vs. 1283) suggested that the transcript levels of key regulatory genes, including transcription factors and signaling genes involved in stem development in alfalfa, especially secondary xylem development, may be regulated by microRNAs.