Transcriptome Analysis in Brassica rapa under the Abiotic Stresses Using Brassica 24K Oligo Microarray
Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequenc...
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| Published in | Molecules and cells Vol. 26; no. 6; pp. 595 - 605 |
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| Main Authors | , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
한국분자세포생물학회
31.12.2008
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1016-8478 0219-1032 |
| DOI | 10.1016/s1016-8478(23)14042-8 |
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| Abstract | Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4℃), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa. |
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| AbstractList | Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4˚C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa. KCI Citation Count: 86 Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4 degrees C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa. Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4℃), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa. Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4 degrees C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa.Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4 degrees C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa. |
| Author | Hur, Y.K. (Chungnam National University, Daejeon, Republic of Korea) Park, B.S. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea), E-mail: pbeom@rda.go.kr Kwon, S.J. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Lim, M.H. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Mun, J.H. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Kim, H.U. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Lee, S.I. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Lee, S.C. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Jin, M.A. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Kim, J.S. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) Kim, Y.K. (GreenGene Biotech Inc. Genomics and Genetics Institute, Yongin, Republic of |
| Author_xml | – sequence: 1 fullname: Lee, S.C. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 2 fullname: Lim, M.H. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 3 fullname: Kim, J.A. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 4 fullname: Lee, S.I. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 5 fullname: Kim, J.S. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 6 fullname: Jin, M.A. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 7 fullname: Kwon, S.J. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 8 fullname: Mun, J.H. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 9 fullname: Kim, Y.K. (GreenGene Biotech Inc. Genomics and Genetics Institute, Yongin, Republic of Korea) – sequence: 10 fullname: Kim, H.U. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea) – sequence: 11 fullname: Hur, Y.K. (Chungnam National University, Daejeon, Republic of Korea) – sequence: 12 fullname: Park, B.S. (National Institute of Agricultural Biotechnology, RDA, Suwon, Republic of Korea), E-mail: pbeom@rda.go.kr |
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| SubjectTerms | BRASSICA CAMPESTRIS Brassica rapa - genetics Cold Temperature Droughts ESTRES Gene Expression Profiling Gene Expression Regulation, Plant Genes, Plant microarray Oligonucleotide Array Sequence Analysis Plant Proteins - genetics Reverse Transcriptase Polymerase Chain Reaction Sodium Chloride - pharmacology STRESS Stress, Physiological - genetics transcriptome 생물학 |
| Title | Transcriptome Analysis in Brassica rapa under the Abiotic Stresses Using Brassica 24K Oligo Microarray |
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