Eveland, A. L., Satoh-Nagasawa, N., Goldschmidt, A., Meyer, S., Beatty, M., Sakai, H., Ware, D. H., Jackson, D. P. (September 2010) Digital Gene Expression Signatures for Maize Development. Plant Physiology, 154 (3). pp. 1024-1039. ISSN 0032-0889
Abstract
Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression (DGE) profiles using Illumina's high-throughput sequencing technology and the newly-assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in axillary meristem determinacy. The RA3 gene encodes a trehalose-6-phosphate-phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of DGE libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20-21nt reads with frequencies spanning four orders of magnitude. Unique sequence tags were anchored to 3'-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of non-redundant signature tags to the maize genome, which associated with 37,117 gene models and un-annotated regions of expression. 66% of maize genes were detected by at least nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis and rice in functional analyses of differentially expressed maize genes. Results from this study provide a basis for analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene.
| Item Type: | Paper |
|---|---|
| Subjects: | organism description > plant > maize bioinformatics > genomics and proteomics > annotation > sequence annotation therapies > stem cells |
| CSHL Authors: | |
| Communities: | CSHL Post Doctoral Fellows CSHL labs > Jackson lab CSHL labs > Ware lab |
| Depositing User: | CSHL Librarian |
| Date: | 10 September 2010 |
| Date Deposited: | 29 Sep 2011 19:12 |
| Last Modified: | 07 Apr 2015 20:19 |
| PMCID: | PMC2971585 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/15408 |
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