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Published on February 16, 2007; 10.1104/pp.106.094334

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Received December 7, 2006
Accepted February 5, 2007

Assessing the Efficiency of RNA Interference for Maize Functional Genomics

Karen McGinnis , Nick Murphy , Alvar R. Carlson , Anisha Akula , Chakradhar Akula , Heather Basinger , Michelle Carlson , Peter Hermanson , Nives Kovacevic , M. Annie McGill , Vishwas Seshadri , Jessica Yoyokie , Karen Cone , Heidi F Kaeppler , Shawn M Kaeppler , and Nathan M Springer *

Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721; Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706; Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108; Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211

* Corresponding author; email: springer{at}umn.edu.

A large-scale functional genomics project was initiated to study the function of chromatin-related genes in Zea mays. Transgenic lines containing short gene segments in inverted repeat orientation designed to reduce expression of target genes by RNA interference (RNAi) were isolated, propagated, and analyzed in a variety of assays. Analysis of the selectable marker expression over multiple generations revealed that most transgenes were transmitted faithfully, whereas some displayed reduced transmission or transgene silencing. A range of target-gene silencing efficiencies, from non-detectable silencing to nearly complete silencing, were revealed by semi-quantitative RT-PCR analysis of transcript abundance for the target gene. In some cases, the RNAi construct was able to cause a reduction in the steady state RNA levels of not only the target gene, but also another closely related gene. Correlation of silencing efficiency with expression level of the target gene and sequence features of the inverted repeat did not reveal any factors capable of predicting the silencing success of a particular RNAi-inducing construct. The frequencies of success of this large-scale project in maize, together with parameters for optimization at various steps, should serve as a useful framework for designing future RNAi-based functional genomics projects in crop plants.




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M. Dafny-Yelin, S.-M. Chung, E. L. Frankman, and T. Tzfira
pSAT RNA Interference Vectors: A Modular Series for Multiple Gene Down-Regulation in Plants
Plant Physiology, December 1, 2007; 145(4): 1272 - 1281.
[Abstract] [Full Text] [PDF]


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