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      Overexpression of miR156 in switchgrass ( Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production

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          Abstract

          Switchgrass ( Panicum virgatum L.) has been developed into a dedicated herbaceous bioenergy crop. Biomass yield is a major target trait for genetic improvement of switchgrass. microRNAs have emerged as a prominent class of gene regulatory factors that has the potential to improve complex traits such as biomass yield. A miR156b precursor was overexpressed in switchgrass. The effects of miR156 overexpression on SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes were revealed by microarray and quantitative RT-PCR analyses. Morphological alterations, biomass yield, saccharification efficiency and forage digestibility of the transgenic plants were characterized. miR156 controls apical dominance and floral transition in switchgrass by suppressing its target SPL genes. Relatively low levels of miR156 overexpression were sufficient to increase biomass yield while producing plants with normal flowering time. Moderate levels of miR156 led to improved biomass but the plants were non-flowering. These two groups of plants produced 58%–101% more biomass yield compared with the control. However, high miR156 levels resulted in severely stunted growth. The degree of morphological alterations of the transgenic switchgrass depends on miR156 level. Compared with floral transition, a lower miR156 level is required to disrupt apical dominance. The improvement in biomass yield was mainly because of the increase in tiller number. Targeted overexpression of miR156 also improved solubilized sugar yield and forage digestibility, and offered an effective approach for transgene containment.

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          miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana.

          The FT gene integrates several external and endogenous cues controlling flowering, including information on day length. A complex of the mobile FT protein and the bZIP transcription factor FD in turn has a central role in activating genes that execute the switch from vegetative to reproductive development. Here we reveal that microRNA156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes not only act downstream of FT/FD, but also define a separate endogenous flowering pathway. High levels of miR156 in young plants prevent precocious flowering. A subsequent day length-independent decline in miR156 abundance provides a permissive environment for flowering and is paralleled by a rise in SPL levels. At the shoot apex, FT/FD and SPLs converge on an overlapping set of targets, with SPLs directly activating flower-promoting MADS box genes, providing a molecular substrate for both the redundant activities and the feed-forward action of the miR156/SPL and FT/FD modules in flowering control.
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            Specific effects of microRNAs on the plant transcriptome.

            Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their targets. This is consistent with their primary mode of action being cleavage of target mRNAs, similar to that induced by perfectly complementary small interfering RNAs (siRNAs). However, there are natural targets with up to five mismatches. Furthermore, artificial siRNAs can have substantial effects on so-called off-targets, to which they have only limited complementarity. By analyzing the transcriptome of plants overexpressing different miRNAs, we have deduced a set of empirical parameters for target recognition. Compared to artificial siRNAs, authentic plant miRNAs appear to have much higher specificity, which may reflect their coevolution with the remainder of the transcriptome. We also demonstrate that miR172, previously thought to act primarily by translational repression, can efficiently guide mRNA cleavage, although the effects on steady-state levels of target transcripts are obscured by strong feedback regulation. This finding unifies the view of plant miRNA action.
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              Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs

              MicroRNAs (miRNAs) are a class of small non-coding RNAs with a critical role in development and environmental responses. Efficient and reliable detection of miRNAs is an essential step towards understanding their roles in specific cells and tissues. However, gel-based assays currently used to detect miRNAs are very limited in terms of throughput, sensitivity and specificity. Here we provide protocols for detection and quantification of miRNAs by RT-PCR. We describe an end-point and real-time looped RT-PCR procedure and demonstrate detection of miRNAs from as little as 20 pg of plant tissue total RNA and from total RNA isolated from as little as 0.1 μl of phloem sap. In addition, we have developed an alternative real-time PCR assay that can further improve specificity when detecting low abundant miRNAs. Using this assay, we have demonstrated that miRNAs are differentially expressed in the phloem sap and the surrounding vascular tissue. This method enables fast, sensitive and specific miRNA expression profiling and is suitable for facilitation of high-throughput detection and quantification of miRNA expression.
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                Author and article information

                Journal
                Plant Biotechnol J
                Plant Biotechnol. J
                pbi
                Plant Biotechnology Journal
                Blackwell Publishing Ltd (Oxford, UK )
                1467-7644
                1467-7652
                May 2012
                : 10
                : 4
                : 443-452
                Affiliations
                [1 ]Forage Improvement Division, The Samuel Roberts Noble Foundation Ardmore, OK, USA
                [2 ]Department of Biochemistry and Molecular Biology, Oklahoma State University Stillwater, OK, USA
                [3 ]Plant Biology Division, The Samuel Roberts Noble Foundation Ardmore, OK, USA
                [4 ]BioEnergy Science Center Oak Ridge, TN, USA
                [5 ]Department of Plant Sciences, University of Tennessee Knoxville, TN, USA
                Author notes
                Correspondence (Tel 1-580-224 6830; fax 1-580-224 6802; email zywang@ 123456noble.org )
                Article
                10.1111/j.1467-7652.2011.00677.x
                3489066
                22239253
                469036c9-1daa-4c91-baaf-78f7ad27bf5c
                © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd

                Re-use of this article is permitted in accordance with the Terms and Conditions set out at http://wileyonlinelibrary.com/onlineopen#OnlineOpen_Terms

                History
                : 10 October 2011
                : 08 December 2011
                : 12 December 2011
                Categories
                Research Articles

                Biotechnology
                mir156,microrna,panicum virgatum,biofuel crop,transgenic switchgrass,biomass
                Biotechnology
                mir156, microrna, panicum virgatum, biofuel crop, transgenic switchgrass, biomass

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