產品資訊 > 水稻表達譜晶片 Rice OneArray® v1

 
  Rice microarray for gene expression   水稻表達譜晶片v1 的探針設計是 參考 RGAP v6.1BGI 2008 基因體資料庫, 同時涵蓋 JaponicaIndica 兩個水稻品種的資訊。 設計原理採用 “一個基因,一個探針” 的概念,以 IMPORT 專利技術針對具有 GO (Gene Ontology) 資訊的基因序列設計高專一性探針, 並以自主的高速佈放技術生產, 為當前具 GO 資訊基因涵蓋度最廣的表達譜晶片。  
 
 
水稻表達譜晶片 v1 探針內容
探針種類 探針數
  基因探針設計資料庫: 21,179
          - RGAP v6.1
          - BGI 2008
  控制探針數 824
  總探針數 22,003


  基 因 探 針

水稻表達譜晶片 v1 的探針設計, 是華聯技術團隊參考 RGAP v6.1BGI 2008 基因體資料庫進行設計, 以具有 GO 資訊的基因序列為主, 藉由經年累積的經驗所研發之基因註解運算流程,設計具高度專一性的長鏈 60 個鹼基寡核酸 (sense-strand) 的基因探針, 內容包含 JaponicaIndica 兩個水稻品種, 每一個探針對其來源資料庫的目標基因皆具高度專一性,避免非目標基因的雜交影響。

此外,華聯專業團隊建構 ”華聯探針註解搜尋引擎”(PASS) 網站,方便使用者查詢各探針相對應於 NCBIEnsembl 資料庫的詳細註解。


  控 制 探 針

為確保晶片數據品質,華聯技術團隊經過一連串的測試及驗證,設計一系列的品質控制探針, 以監控完整的晶片實驗步驟,包含樣本 RNA 完整性、樣本 RNA 放大流程、螢光標記效率、晶片雜交、晶片掃描等。
 
 

使用RiOA文獻 ( 4 )

 BMC Plant Biology. 2015, 15:156. doi: 10.1186/s12870-015-0515-4.
 The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons 
 Xiuying Gao, Xiaojun Zhang, Hongxia Lan, Ji Huang, Jianfei Wang, Hongsheng Zhang
  Abstract
Background: Grain length, as a critical trait for rice grain size and shape, has a great effect on grain yield and appearance quality. Although several grain size/shape genes have been cloned, the genetic interaction among these genes and the molecular mechanisms of grain size/shape architecture have not yet to be explored. Results: To investigate the genetic interaction between two major grain length loci of rice, GS3 and qGL3, we developed two near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3) and NIL-qgl3 (gs3/qgl3), in the genetic background of 93¡V11 (gs3/qGL3) by conventional backcrossing and marker-assisted selection (MAS). Another NIL-GS3/qgl3 (GS3/qgl3) was developed by crossing NIL-GS3 with NIL-qgl3 and using MAS. By comparing the grain lengths of 93¡V11, NIL-GS3, NIL-qgl3 and NIL-GS3/qgl3, we investigated the effects of GS3, qGL3 and GS3 ¡Ñ qGL3 interaction on grain length based on two-way ANOVA. We found that GS3 and qGL3 had additive effects on rice grain length regulation. Comparative analysis of primary panicle transcriptomes in the four NILs revealed that the genes affected by GS3 and qGL3 partially overlapped, and both loci might be involved in brassinosteroid signaling. Conclusion: Our data provide new information to better understand the rice grain length regulation mechanism and help rice breeders improve rice yield and appearance quality by molecular design breeding.
   

 PLoS One. 2015, 10(7):e0131391. doi: 10.1371/journal.pone.0131391. eCollection 2015.
 Comparative Transcriptome Analysis of Shoots and Roots of TNG67 and TCN1 Rice Seedlings under Cold Stress and Following Subsequent Recovery: Insights into Metabolic Pathways, Phytohormones, and Transcription Factors
 
 
 Yun-Wei Yang, Hung-Chi Chen, Wei-Fu Jen, Li-Yu Liu, Men-Chi Chang
  Abstract
Cold stress affects rice growth, quality and yield. The investigation of genome-wide gene expression is important for understanding cold stress tolerance in rice. We performed comparative transcriptome analysis of the shoots and roots of 2 rice seedlings (TNG67, cold-tolerant; and TCN1, cold-sensitive) in response to low temperatures and restoration of normal temperatures following cold exposure. TNG67 tolerated cold stress via rapid alterations in gene expression and the re-establishment of homeostasis, whereas the opposite was observed in TCN1, especially after subsequent recovery. Gene ontology and pathway analyses revealed that cold stress substantially regulated the expression of genes involved in protein metabolism, modification, translation, stress responses, and cell death. TNG67 takes advantage of energy-saving and recycling resources to more efficiently synthesize metabolites compared with TCN1 during adjustment to cold stress. During recovery, expression of OsRR4 type-A response regulators was upregulated in TNG67 shoots, whereas that of genes involved in oxidative stress, chemical stimuli and carbohydrate metabolic processes was downregulated in TCN1. Expression of genes related to protein metabolism, modification, folding and defense responses was upregulated in TNG67 but not in TCN1 roots. In addition, abscisic acid (ABA)-, polyamine-, auxin- and jasmonic acid (JA)-related genes were preferentially regulated in TNG67 shoots and roots and were closely associated with cold stress tolerance. The TFs AP2/ERF were predominantly expressed in the shoots and roots of both TNG67 and TCN1. The TNG67-preferred TFs which express in shoot or root, such as OsIAA23, SNAC2, OsWRKY1v2, 24, 53, 71, HMGB, OsbHLH and OsMyb, may be good candidates for cold stress tolerance-related genes in rice. Our findings highlight important alterations in the expression of cold-tolerant genes, metabolic pathways, and hormone-related and TF-encoding genes in TNG67 rice during cold stress and recovery. The cross-talk of hormones may play an essential role in the ability of rice plants to cope with cold stress.
   

 Plant Molecular Biology. 2014 Jul 8.
 Expression of a gene encoding a rice RING zinc-finger protein, OsRZFP34, enhances stomata opening
 
 
 Kuo‑Hsuan Hsu, Chia‑Chin Liu, Shaw‑Jye Wu, Ying‑Yu Kuo, Chung‑An Lu, Ching‑Rong Wu, Pei‑Jyun Lian, Chwan‑Yang Hong, Yi‑Ting Ke, Juin‑Hua Huang, Ching‑Hui Yeh
  Abstract
By oligo microarray expression profiling, we identified a rice RING zinc-finger protein (RZFP), OsRZFP34, whose gene expression increased with high temperature or abscisic acid (ABA) treatment. As compared with the wild type, rice and Arabidopsis with OsRZFP34 overexpression showed increased relative stomata opening even with ABA treatment. Furthermore, loss-of-function mutation of OsRZFP34 and AtRZFP34 (At5g22920), anOsRZFP34 homolog in Arabidopsis, decreased relative stomata aperture under nonstress control conditions. Expressing OsRZFP34 in atrzfp34 reverted the mutant phenotype to normal, which indicates a conserved molecular function between OsRZFP34 and AtRZFP34. Analysis of water loss and leaf temperature under stress conditions revealed a higher evaporation rate and cooling effect in OsRZFP34-overexpressing Arabidopsis and ricethan the wild type, atrzfp34 and osrzfp34. Thus, stomata opening, enhanced leaf cooling, and ABA insensitivity was conserved with OsRZFP34 expression. Transcription profiling of transgenic rice overexpressing OsRZFP34 revealed many genes involved in OsRZFP34-mediated stomatal movement. Several genes upregulated or downregulated in OsRZFP34-overexpressing plants were previously implicated in Ca2+ sensing, K+ regulator, and ABA response. We suggest that OsRZFP34 may modulate these genes to control stomata opening.
   

 BMC Research Notes. Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues.
 2014, 7(1):15. doi: 10.1186/1756-0500-7-15
 
 
 Jia-Shing Chen, Shang-Chi Lin, Chia-Ying Chen, Yen-Ting Hsieh, Ping-Hui Pai, Long-Kung Chen, Shengwan Lee
  Abstract
BACKGROUND: Rice is one of the major crop species in the world helping to sustain approximately half of the global population's diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray® microarray platform which is suitable for two major rice subspecies, japonica and indica. RESULTS: The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R = 0.95, p < 0.001***). CONCLUSION: The rice OneArray® 22 K microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in rice tissues. The rice OneArray® microarray platform revealed high specificity and sensitivity. Additional information for the rice OneArray® microarray can be found at http://www.phalanx.com.tw/index.php.