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 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.
Lee
Sang-Choon
SC
National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea.
Lim
Myung-Ho
MH
Kim
Jin A
JA
Lee
Soo-In
SI
Kim
Jung Sun
JS
Jin
Mina
M
Kwon
Soo-Jin
SJ
Mun
Jeong-Hwan
JH
Kim
Yeon-Ki
YK
Kim
Hyun Uk
HU
Hur
Yoonkang
Y
Park
Beom-Seok
BS
D029741:Brassica rapa / Q000235:genetics*; D003080:Cold Temperature; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000235:genetics*
D010940:Plant Proteins; D012965:Sodium Chloride