Download 200505060356110.RiceGeneExpression

Analysis of the rice gene expression profile by 60K microarray
Kim Yong-Hwan1), Lee Jung-Sook,1) Yoon Ung-Han1), Lee Kang-Seob1), Nahm Back-Hie 2), Song Sang-Ik 2),
Choi Sang-Bong 2), Ahn Joong-Hoon 3)
1) National Institute of Agricultural Biotechnology, RDA, Suwon, 441-707, South Korea
2) Myoung Ji University, Yong In , 449-728, South Korea
3) KonKuk University, Seoul,143-701, South Korea
Results
Abstract
Hierarchical clustering of Expression Profiling
Treated with five Plant hormones
Rice 60K Oligomer Microarray
In order to screen of tissue and plant hormone
specific genes from rice, 60K oligomer chips were
used. 790 regeneration tissue specific, 4,039 flower
specific, 2,173 root specific and 2,766 leaf specific
genes were isolated. Among the tissue specific
expressed genes, 431 genes were identified as
transcription factors. High expressed (2 fold up)
3,287 genes treated by Plant hormones (Jasmonic
acid, Salicylic acid, Abscisci acid and Methyl
jasmonate) were profiled. 249 out of 3,287 genes
were identified as transcription factor. All information
of expressed gene of rice DB will be opened at NABIC
(National Agricultural Biotechnology Information
Center) site (http://www.niab.go.kr )
• 64,904 spots / two slides,
Whole Genes (8000)
After 1 hr
ET JA SA ABAmJA
•48 blocks of 12 rows and 4 columns.
•676 (26x26) spots
• 60,100 oligomers
- Known and predicted genes:
57,734
- Antisense :
2,310
- Randomized control DNA :
66
- Blank spots:
•Average diameter of 120 um.
•70mers with average Tm of 68+/-5° C
•Effective Cost : 10,000 won/gene X 57,000 genes
2,284
119
282
601
46
258
909
525
2,102
95
342
1,003
3,287
: 1mM ethephon (Ethylene)
: 100mM jasmonic acid
: 100mM salicylic acid
: 100mM abscisic acid
: 100mM methyl jasmonate
Hierarchical clustering of transcription factors
Treated with five Plant hormones :
Transcription Factors (600)
After 1 hr
ET JA SA ABAmJA
Group
Flower
Heading
Before
Pollination
Etiolated
Leaf
1.6X Up 1.6X Down Total
ERF/AP2
BHLH
bZIP
C2H2
C3H
Myb
MybRelated
NAC
WRKY
Subtotal
Etc
callus
Flower
After
Pollination
Leaf
Dong-Jin Byeo
Hierarchical clustering of tissue specific Expression Profiling
7
6
3
7
19
4
3
5
5
61
10
16
6
9
17
8
17
22
9
16
36
12
4
8
11
92
7
13
16
153
96
Total
- Rice Whole genome Oligomer Chip
- 64,000 spots in two slides
790
243
1,501
49
84
Tissue and stage specific transcriptome profiling
with Rice 60K Microarrary
root
 Rice 60K oligomer chip
ABA
ET
JA
mJA
SA
ET
JA
SA
ABA
mJA
Reg.
callus
 Rice variety :
2X Up 2X Down Total
Total
4,190
Germina
ting seed
Materials and Methods
Group
249
Callus
Hd Lf Rt Reg
Leaf
Heading
- Design of 70mers with Gene Prediction
 Experimental procedure
callus
- Dye Labeling
Reg.
callus
1.6 fold up regulated transcription factors
Hierachial
Clustering
Hormone
ABA
ET
JA
mJA
SA
Toatal
TFs
- Hybridization
- Two dye analysis ; Cy3 (control) and Cy5 (Treatment)
Root
 Microarray analysis:
- Data capturing with GenePix Pro 5.0
- Data processing with Acuity v.3.0
WRKY
3
ERF
1
NAC
bHLH
Hierarchical clustering of significant spots (12,289)
were performed.
Total
1
5
5
2
5
1
7
2
3
5
2
5
2
1
11
4
13
5
1
28
- Statistical Analysis
Conclusion
Flower stage specific (4,039)
Management system of gene expression profile
of rice at NABIC
Root specific a(2,173)
Leaf specific (2,766)
.
 Expressed gene profile of rice
- Tissue specific expression (9,768) ;
Regeneration tissue
Flower
Root
Leaf
Transcription factor
; 790
; 4,039
; 2,173
; 2,766
; 431
Root specific b(*)
 Gene expression level
check
Reg. Callus specific (790)
Hierarchical clustering of transcription factors at rice tissues
Putative transcription factors in Rice 60K Microarray: 2,528
Number of TFs significantly changed between tissue comparison
 Popup window
shows detailed
microarray data
- Two fold change by Hormone treatment (3,287)
Transcription factor
; 249
Regeneration group (9)
 Future plan
To construct the expression gene network in rice, we
will used Ac/Ds mutant lines and transgenic rice as
many as possible and the obtained DNA chip data will
be opened at NIAB home page (NABIC)
Root specific group (93)
 Sample,
Labeling,
Hybridization,
Scan
information
Leaf specific group (110)
Flower specific
group (130)
National Institute of Agricultural Biotechnology (NIAB)