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Comparative Study
. 2006 Feb 22:6:4.
doi: 10.1186/1471-2229-6-4.

Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja

Wei Ji  1 , Yong Li, Jie Li, Cui-hong Dai, Xi Wang, Xi Bai, Hua Cai, Liang Yang, Yan-ming Zhu
Affiliations
Comparative Study

Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja

Wei Ji et al. BMC Plant Biol. .

Abstract

Background: Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture. Wild soybean (Glycine soja) can survive in highly saline conditions, therefore provides an ideal candidate plant system for salt tolerance gene mining.

Results: As a first step towards the characterization of genes that contribute to combating salinity stress, we constructed a full-length cDNA library of Glycine soja (50109) leaf treated with 150 mM NaCl, using the SMART technology. Random expressed sequence tag (EST) sequencing of 2,219 clones produced 2,003 cleaned ESTs for gene expression analysis. The average read length of cleaned ESTs was 454 bp, with an average GC content of 40%. These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets. The resulting unigenes were categorized according to the Gene Ontology (GO) hierarchy. The potential roles of gene products associated with stress related ESTs were discussed. We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm. Most expressed sequences from wild soybean exhibited similarity with soybean. All our EST data are available on the Internet (GenBank_Accn: DT082443-DT084445).

Conclusion: The Glycine soja ESTs will be used to mine salt tolerance gene, whose full-length cDNAs will be obtained easily from the full-length cDNA library. Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybean's expression profile using the soybean's gene chip. This will provide opportunities to understand the genetic mechanisms underlying stress response of plants.

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Figures

Figure 1
Figure 1
Distribution and number of clustered sequences.
Figure 2
Figure 2
Representation of Gene Ontology (GO) mapping results for Glycine soja non-redundant ESTs.
See this image and copyright information in PMC

References

    1. John CushmanC, Hans BohnertJ. Genomic approaches to plant stress tolerance. Genome studies and molecular genetics, Current Opinion in Plant Biology. 2000;3:117–124. - PubMed
    1. Frova C, Caffulli A, Pallavera E. Mapping quantitative trait loci for tolerance to abiotic stresses in maize. J Exp Zool. 1999;282:164–170. doi: 10.1002/(SICI)1097-010X(199809/10)282:1/2<164::AID-JEZ18>3.0.CO;2-U. - DOI
    1. Cushman JC, Bohnert HJ. Genomics approaches to plant strss. Curr Opin Plant Biol. 2000;3:117–124. doi: 10.1016/S1369-5266(99)00052-7. - DOI - PubMed
    1. Nuccio ML, Rhodes D, McNeil SD, Hanson AD. Metabolic engineering of plants for osmotic stress resistance. Curr Opin Plant Biol. 1998;2:128–134. doi: 10.1016/S1369-5266(99)80026-0. - DOI - PubMed
    1. Bouchez D, Höfte H. Functional genomics in plants. Plant Physiol. 1998;118:725–732. doi: 10.1104/pp.118.3.725. - DOI - PMC - PubMed

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