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Mol. Cells 2012; 34(1): 53-59

Published online July 31, 2012

https://doi.org/10.1007/s10059-012-0068-4

© The Korean Society for Molecular and Cellular Biology

Screening of Tissue-Specific Genes and Promoters in Tomato by Comparing Genome Wide Expression Profiles of Arabidopsis Orthologues

Chan Ju Lim1, Ha Yeon Lee1, Woong Bom Kim1, Bok-Sim Lee1, Jungeun Kim1,2, Raza Ahmad1, Hyun A Kim1,3, So Young Yi1, Cheol-Goo Hur1,2, and Suk-Yoon Kwon1,3,*

1Green Bio Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea, 2Bioinformatics, University of Science and Technology, Daejeon 305-350, Korea, 3Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea

Correspondence to : *Correspondence: sykwon@kribb.re.kr

Received: March 5, 2012; Revised: May 10, 2012; Accepted: May 14, 2012

Abstract

Constitutive overexpression of transgenes occasionally interferes with normal growth and developmental processes in plants. Thus, the development of tissue-specific promoters that drive transgene expression has become agriculturally important. To identify tomato tissue-specific promoters, tissue-specific genes were screened using a series of in silico-based and ex-perimental procedures, including genome-wide orthologue searches of tomato and Arabidopsis databases, isolation of tissue-specific candidates using an Arabidopsis microarray database, and validation of tissue specificity by reverse transcrip-tion-polymerase chain reaction (RT-PCR) analysis and promoter assay. Using these procedures, we found 311 tissue-specific candidate genes and validated 10 tissue-specific genes by RT-PCR. Among these identified genes, histochemical analysis of five isolated promoter::GUS transgenic tomato and Arabidopsis plants revealed that their promoters have different but distinct tissue-specific activities in anther, fruit, and root, respectively. Therefore, it appears these in silico-based screening approaches in addition to the identification of new tissue-specific genes and promoters will be helpful for the further development of tailored crop development.

Keywords orthologue search, promoter, tissue-specific gene, tomato

Article

Research Article

Mol. Cells 2012; 34(1): 53-59

Published online July 31, 2012 https://doi.org/10.1007/s10059-012-0068-4

Copyright © The Korean Society for Molecular and Cellular Biology.

Screening of Tissue-Specific Genes and Promoters in Tomato by Comparing Genome Wide Expression Profiles of Arabidopsis Orthologues

Chan Ju Lim1, Ha Yeon Lee1, Woong Bom Kim1, Bok-Sim Lee1, Jungeun Kim1,2, Raza Ahmad1, Hyun A Kim1,3, So Young Yi1, Cheol-Goo Hur1,2, and Suk-Yoon Kwon1,3,*

1Green Bio Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea, 2Bioinformatics, University of Science and Technology, Daejeon 305-350, Korea, 3Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea

Correspondence to:*Correspondence: sykwon@kribb.re.kr

Received: March 5, 2012; Revised: May 10, 2012; Accepted: May 14, 2012

Abstract

Constitutive overexpression of transgenes occasionally interferes with normal growth and developmental processes in plants. Thus, the development of tissue-specific promoters that drive transgene expression has become agriculturally important. To identify tomato tissue-specific promoters, tissue-specific genes were screened using a series of in silico-based and ex-perimental procedures, including genome-wide orthologue searches of tomato and Arabidopsis databases, isolation of tissue-specific candidates using an Arabidopsis microarray database, and validation of tissue specificity by reverse transcrip-tion-polymerase chain reaction (RT-PCR) analysis and promoter assay. Using these procedures, we found 311 tissue-specific candidate genes and validated 10 tissue-specific genes by RT-PCR. Among these identified genes, histochemical analysis of five isolated promoter::GUS transgenic tomato and Arabidopsis plants revealed that their promoters have different but distinct tissue-specific activities in anther, fruit, and root, respectively. Therefore, it appears these in silico-based screening approaches in addition to the identification of new tissue-specific genes and promoters will be helpful for the further development of tailored crop development.

Keywords: orthologue search, promoter, tissue-specific gene, tomato

Mol. Cells
May 31, 2022 Vol.45 No.5, pp. 273~352
COVER PICTURE
Fe2+ ion depletion-induced expression of BΔGFP at the early stage of leaf development (Choi et al., pp. 294-305).

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