An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants
Article first published online: 7 APR 2010
© 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd
The Plant Journal
Volume 63, Issue 1, pages 86–99, July 2010
How to Cite
Libault, M., Farmer, A., Joshi, T., Takahashi, K., Langley, R. J., Franklin, L. D., He, J., Xu, D., May, G. and Stacey, G. (2010), An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. The Plant Journal, 63: 86–99. doi: 10.1111/j.1365-313X.2010.04222.x
- Issue published online: 30 JUN 2010
- Article first published online: 7 APR 2010
- Received 18 January 2010; revised 25 March 2010; accepted 31 March 2010; published online 14 May 2010.
- gene expression atlas;
- comparative genomic;
- transcription factors;
Soybean (Glycine max L.) is a major crop providing an important source of protein and oil, which can also be converted into biodiesel. A major milestone in soybean research was the recent sequencing of its genome. The sequence predicts 69 145 putative soybean genes, with 46 430 predicted with high confidence. In order to examine the expression of these genes, we utilized the Illumina Solexa platform to sequence cDNA derived from 14 conditions (tissues). The result is a searchable soybean gene expression atlas accessible through a browser (http://digbio.missouri.edu/soybean_atlas). The data provide experimental support for the transcription of 55 616 annotated genes and also demonstrate that 13 529 annotated soybean genes are putative pseudogenes, and 1736 currently unannotated sequences are transcribed. An analysis of this atlas reveals strong differences in gene expression patterns between different tissues, especially between root and aerial organs, but also reveals similarities between gene expression in other tissues, such as flower and leaf organs. In order to demonstrate the full utility of the atlas, we investigated the expression patterns of genes implicated in nodulation, and also transcription factors, using both the Solexa sequence data and large-scale qRT-PCR. The availability of the soybean gene expression atlas allowed a comparison with gene expression documented in the two model legume species, Medicago truncatula and Lotus japonicus, as well as data available for Arabidopsis thaliana, facilitating both basic and applied aspects of soybean research.