产品资讯 > 水稻表达谱芯片 Rice OneArrayR v1

 
  Rice microarray for gene expression   华联生技与台湾农委会共同合作开发水稻表达谱芯片。 目前水稻表达谱芯片 v1 的雏型已阶段性完成, 并通过基础的品质验证测试。此雏型芯片的探针设计是参考 RGAP v6.1BGI 2008 基因体资料库, 同时涵盖 JaponicaIndica 两个水稻品种的资讯。 设计原理采用 “一个基因,一个探针” 的概念,以 IMPORT 专利技术针对具有 GO (Gene Ontology) 资讯的基因序列设计高专一性探针, 并以自主的高速布放技术生产,为当前具 GO 资讯基因涵盖度最广的表达谱芯片。 欢迎各方洽询!!  
 
 
水稻表达谱芯片 v1 探针内容
探针种类 探针数
  基因探针设计资料库: 21,179
          - RGAP v6.1
          - BGI 2008
  控制探针数 824
  总探针数 22,003


  基 因 探 针

水稻表达谱芯片 v1 的探针设计, 是华联技术团队参考 RGAP v6.1BGI 2008 基因体资料库进行设计, 以具有 GO 资讯的基因序列为主, 藉由经年累积的经验所研发之基因注解运算流程,设计具高度专一性的长链 60 个碱基寡核酸 (sense-strand) 的基因探针, 内容包含 JaponicaIndica 两个水稻品种, 每一个探针对其来源资料库的目标基因皆具高度专一性,避免非目标基因的杂交影响。

此外,华联专业团队建构 ”华联探针注解搜寻引擎”(PASS) 网站,方便使用者查询各探针相对应于 NCBIEnsembl 资料库的详细注解。


  控 制 探 针

为确保芯片数据品质,华联技术团队经过一连串的测试及验证,设计一系列的品质控制探针, 以监控完整的芯片实验步骤,包含样本 RNA 完整性、样本 RNA 放大流程、萤光标记效率、芯片杂交、芯片扫描等。
 

使用RiOA文献 ( 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 93–11 (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 93–11, NIL-GS3, NIL-qgl3 and NIL-GS3/qgl3, we investigated the effects of GS3, qGL3 and GS3 × 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.