| *Town, Chris Redman, Julia Zhuang, Jun Monaghan, Erin Wang, Wei Moskal, William Wu, Hank Quan, Hui Underwood, Beverly Xiao, Yongli |
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A variety of platforms, including cDNA microarray, Affymetrix GeneChip, whole genome tiling array, massively parallel signature sequencing, have been used extensively to study gene expression in Arabidopsis thaliana. However, there are still many genes in the Arabidopsis genome that could not be profiled effectively by any of these methods, generally due to the low abundance of their transcripts in mRNA populations. We are therefore generating expression profiles by quantitative real time PCR (qRT-PCR) which is about 2-3 orders of magnitude more sensitive than hybridization-based technologies for many of the function of unknown genes in Arabidopsis currently lacking reliable expression data. To date, we have performed qRT-PCR on about 2,000 genes using mRNAs from leaf, root, bud, silique and T87 cell culture and seedlings treated with IAA, SA and salt. Over 90% of the genes were expressed in at least one of our current cDNA populations and ~ 40% of them showed differential expression in at least 2 out of 8 conditions. We are using co-expression analysis to associate these low-expressing genes with functionally annotated genes and pathways. In addition, we have developed a high throughput pipeline to generate promoter-reporter constructs and transgenic Arabidopsis plants for a subset of these genes of unknown function. So far, promoters from 587 genes have been cloned into a GFP reporter construct and 495 have been transformed into Arabidopsis. All the GFP expression patterns detected in these transgenic plants are localized to small regions of tissues and cell types. Both the qPCR and reporter construct data can be found at www.tigr.org/tdb/e2k1/ath1/qpcr/index.shtml. Supported by NSF 2010.
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